*)
;;
esac
- # -malign-double for x86 systems
- ACX_CHECK_CC_FLAGS(-malign-double,align_double,xCFLAGS="$xCFLAGS -malign-double")
fi
if test $enable_fortran = yes; then
fi
fi
+if test $enable_apple_64bit = yes; then
+ ACX_CHECK_CC_FLAGS(-m64,m64,xCFLAGS="$xCFLAGS -m64")
+fi
+
CPU_FLAGS=""
if test "$GCC" = "yes"; then
#
Summary: Molecular dynamics package (parallel)
Name: gromacs-mpi
-Version: 3.3
+Version: 4.0
Release: 1
Copyright: GPL
Group: Applications/Science
#
Summary: Molecular dynamics package (non-parallel version)
Name: gromacs
-Version: 3.3
+Version: 4.0
Release: 1
Copyright: GPL
Group: Applications/Science
set dir = $cwd
-set VER = 3.3
+set VER = 4.0
set MANDIR = online
set HTML = $cwd/html
set HTMLOL = $HTML/$MANDIR
set dir = $cwd
-set VER = 3.3
+set VER = 4.0
set TEXIDX = proglist.tex
set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
g_saltbr|computes salt bridges
g_sas|computes solvent accessible surface area
g_order|computes the order parameter per atom for carbon tails
+g_principal|calculates axes of inertia for a group of atoms
g_rdf|calculates radial distribution functions
g_sdf|calculates solvent distribution functions
g_sgangle|computes the angle and distance between two groups
#! /bin/sh
# Attempt to guess a canonical system name.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
-# Inc.
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# Free Software Foundation, Inc.
-timestamp='2007-12-12'
+timestamp='2008-04-14'
# This file is free software; you can redistribute it and/or modify it
# under the terms of the GNU General Public License as published by
GNU config.guess ($timestamp)
Originally written by Per Bothner.
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
echo rs6000-ibm-aix3.2
fi
exit ;;
- *:AIX:*:[45])
+ *:AIX:*:[456])
IBM_CPU_ID=`/usr/sbin/lsdev -C -c processor -S available | sed 1q | awk '{ print $1 }'`
if /usr/sbin/lsattr -El ${IBM_CPU_ID} | grep ' POWER' >/dev/null 2>&1; then
IBM_ARCH=rs6000
a.out-i386-linux)
echo "${UNAME_MACHINE}-pc-linux-gnuaout"
exit ;;
- coff-i386)
- echo "${UNAME_MACHINE}-pc-linux-gnucoff"
- exit ;;
"")
# Either a pre-BFD a.out linker (linux-gnuoldld) or
# one that does not give us useful --help.
BePC:BeOS:*:*) # BeOS running on Intel PC compatible.
echo i586-pc-beos
exit ;;
+ BePC:Haiku:*:*) # Haiku running on Intel PC compatible.
+ echo i586-pc-haiku
+ exit ;;
SX-4:SUPER-UX:*:*)
echo sx4-nec-superux${UNAME_RELEASE}
exit ;;
the operating system you are using. It is advised that you
download the most up to date version of the config scripts from
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.guess
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.guess;hb=HEAD
and
- http://savannah.gnu.org/cgi-bin/viewcvs/*checkout*/config/config/config.sub
+ http://git.savannah.gnu.org/gitweb/?p=config.git;a=blob_plain;f=config.sub;hb=HEAD
If the version you run ($0) is already up to date, please
send the following data and any information you think might be
#! /bin/sh
# Configuration validation subroutine script.
# Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999,
-# 2000, 2001, 2002, 2003, 2004, 2005, 2006 Free Software Foundation,
-# Inc.
+# 2000, 2001, 2002, 2003, 2004, 2005, 2006, 2007, 2008
+# Free Software Foundation, Inc.
-timestamp='2007-12-05'
+timestamp='2008-09-08'
# This file is (in principle) common to ALL GNU software.
# The presence of a machine in this file suggests that SOME GNU software
version="\
GNU config.sub ($timestamp)
-Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001, 2002, 2003, 2004, 2005
-Free Software Foundation, Inc.
+Copyright (C) 1992, 1993, 1994, 1995, 1996, 1997, 1998, 1999, 2000, 2001,
+2002, 2003, 2004, 2005, 2006, 2007, 2008 Free Software Foundation, Inc.
This is free software; see the source for copying conditions. There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
| i370 | i860 | i960 | ia64 \
| ip2k | iq2000 \
| m32c | m32r | m32rle | m68000 | m68k | m88k \
- | maxq | mb | microblaze | mcore | mep \
+ | maxq | mb | microblaze | mcore | mep | metag \
| mips | mipsbe | mipseb | mipsel | mipsle \
| mips16 \
| mips64 | mips64el \
- | mips64vr | mips64vrel \
+ | mips64octeon | mips64octeonel \
| mips64orion | mips64orionel \
+ | mips64r5900 | mips64r5900el \
+ | mips64vr | mips64vrel \
| mips64vr4100 | mips64vr4100el \
| mips64vr4300 | mips64vr4300el \
| mips64vr5000 | mips64vr5000el \
| v850 | v850e \
| we32k \
| x86 | xc16x | xscale | xscalee[bl] | xstormy16 | xtensa \
- | z8k)
+ | z8k | z80)
basic_machine=$basic_machine-unknown
;;
m6811 | m68hc11 | m6812 | m68hc12)
| ip2k-* | iq2000-* \
| m32c-* | m32r-* | m32rle-* \
| m68000-* | m680[012346]0-* | m68360-* | m683?2-* | m68k-* \
- | m88110-* | m88k-* | maxq-* | mcore-* \
+ | m88110-* | m88k-* | maxq-* | mcore-* | metag-* \
| mips-* | mipsbe-* | mipseb-* | mipsel-* | mipsle-* \
| mips16-* \
| mips64-* | mips64el-* \
- | mips64vr-* | mips64vrel-* \
+ | mips64octeon-* | mips64octeonel-* \
| mips64orion-* | mips64orionel-* \
+ | mips64r5900-* | mips64r5900el-* \
+ | mips64vr-* | mips64vrel-* \
| mips64vr4100-* | mips64vr4100el-* \
| mips64vr4300-* | mips64vr4300el-* \
| mips64vr5000-* | mips64vr5000el-* \
| sparclite-* \
| sparcv8-* | sparcv9-* | sparcv9b-* | sparcv9v-* | strongarm-* | sv1-* | sx?-* \
| tahoe-* | thumb-* \
- | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* \
+ | tic30-* | tic4x-* | tic54x-* | tic55x-* | tic6x-* | tic80-* | tile-* \
| tron-* \
| v850-* | v850e-* | vax-* \
| we32k-* \
| x86-* | x86_64-* | xc16x-* | xps100-* | xscale-* | xscalee[bl]-* \
| xstormy16-* | xtensa*-* \
| ymp-* \
- | z8k-*)
+ | z8k-* | z80-*)
;;
# Recognize the basic CPU types without company name, with glob match.
xtensa*)
basic_machine=c90-cray
os=-unicos
;;
+ cegcc)
+ basic_machine=arm-unknown
+ os=-cegcc
+ ;;
convex-c1)
basic_machine=c1-convex
os=-bsd
basic_machine=m88k-motorola
os=-sysv3
;;
+ dicos)
+ basic_machine=i686-pc
+ os=-dicos
+ ;;
djgpp)
basic_machine=i586-pc
os=-msdosdjgpp
basic_machine=tic6x-unknown
os=-coff
;;
+ tile*)
+ basic_machine=tile-unknown
+ os=-linux-gnu
+ ;;
tx39)
basic_machine=mipstx39-unknown
;;
basic_machine=z8k-unknown
os=-sim
;;
+ z80-*-coff)
+ basic_machine=z80-unknown
+ os=-sim
+ ;;
none)
basic_machine=none-none
os=-none
| -bosx* | -nextstep* | -cxux* | -aout* | -elf* | -oabi* \
| -ptx* | -coff* | -ecoff* | -winnt* | -domain* | -vsta* \
| -udi* | -eabi* | -lites* | -ieee* | -go32* | -aux* \
- | -chorusos* | -chorusrdb* \
+ | -chorusos* | -chorusrdb* | -cegcc* \
| -cygwin* | -pe* | -psos* | -moss* | -proelf* | -rtems* \
| -mingw32* | -linux-gnu* | -linux-newlib* | -linux-uclibc* \
| -uxpv* | -beos* | -mpeix* | -udk* \
-zvmoe)
os=-zvmoe
;;
+ -dicos*)
+ os=-dicos
+ ;;
-none)
;;
*)
# ltmain.sh - Provide generalized library-building support services.
# NOTE: Changing this file will not affect anything until you rerun configure.
#
-# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005
-# Free Software Foundation, Inc.
+# Copyright (C) 1996, 1997, 1998, 1999, 2000, 2001, 2003, 2004, 2005, 2006,
+# 2007, 2008 Free Software Foundation, Inc.
# Originally by Gordon Matzigkeit <gord@gnu.ai.mit.edu>, 1996
#
# This program is free software; you can redistribute it and/or modify
PROGRAM=ltmain.sh
PACKAGE=libtool
-VERSION="1.5.22 Debian 1.5.22-2"
-TIMESTAMP=" (1.1220.2.365 2005/12/18 22:14:06)"
-
-# See if we are running on zsh, and set the options which allow our
-# commands through without removal of \ escapes.
-if test -n "${ZSH_VERSION+set}" ; then
+VERSION=1.5.26
+TIMESTAMP=" (1.1220.2.492 2008/01/30 06:40:56)"
+
+# Be Bourne compatible (taken from Autoconf:_AS_BOURNE_COMPATIBLE).
+if test -n "${ZSH_VERSION+set}" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on ${1+"$@"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '${1+"$@"}'='"$@"'
setopt NO_GLOB_SUBST
+else
+ case `(set -o) 2>/dev/null` in *posix*) set -o posix;; esac
fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
# Check that we have a working $echo.
if test "X$1" = X--no-reexec; then
# These must not be set unconditionally because not all systems understand
# e.g. LANG=C (notably SCO).
# We save the old values to restore during execute mode.
-if test "${LC_ALL+set}" = set; then
- save_LC_ALL="$LC_ALL"; LC_ALL=C; export LC_ALL
-fi
-if test "${LANG+set}" = set; then
- save_LANG="$LANG"; LANG=C; export LANG
+lt_env=
+for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+do
+ eval "if test \"\${$lt_var+set}\" = set; then
+ save_$lt_var=\$$lt_var
+ lt_env=\"$lt_var=\$$lt_var \$lt_env\"
+ $lt_var=C
+ export $lt_var
+ fi"
+done
+
+if test -n "$lt_env"; then
+ lt_env="env $lt_env"
fi
# Make sure IFS has a sensible default
preserve_args=
lo2o="s/\\.lo\$/.${objext}/"
o2lo="s/\\.${objext}\$/.lo/"
+extracted_archives=
+extracted_serial=0
#####################################
# Shell function definitions:
if eval $OBJDUMP -f $1 | $SED -e '10q' 2>/dev/null | \
$EGREP -e 'file format pe-i386(.*architecture: i386)?' >/dev/null ; then
win32_nmres=`eval $NM -f posix -A $1 | \
- $SED -n -e '1,100{/ I /{s,.*,import,;p;q;};}'`
+ $SED -n -e '1,100{
+ / I /{
+ s,.*,import,
+ p
+ q
+ }
+ }'`
case $win32_nmres in
import*) win32_libid_type="x86 archive import";;
*) win32_libid_type="x86 archive static";;
*) my_xabs=`pwd`"/$my_xlib" ;;
esac
my_xlib=`$echo "X$my_xlib" | $Xsed -e 's%^.*/%%'`
- my_xdir="$my_gentop/$my_xlib"
+ my_xlib_u=$my_xlib
+ while :; do
+ case " $extracted_archives " in
+ *" $my_xlib_u "*)
+ extracted_serial=`expr $extracted_serial + 1`
+ my_xlib_u=lt$extracted_serial-$my_xlib ;;
+ *) break ;;
+ esac
+ done
+ extracted_archives="$extracted_archives $my_xlib_u"
+ my_xdir="$my_gentop/$my_xlib_u"
$show "${rm}r $my_xdir"
$run ${rm}r "$my_xdir"
;;
--version)
- $echo "$PROGRAM (GNU $PACKAGE) $VERSION$TIMESTAMP"
- $echo
- $echo "Copyright (C) 2005 Free Software Foundation, Inc."
- $echo "This is free software; see the source for copying conditions. There is NO"
- $echo "warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
+ echo "\
+$PROGRAM (GNU $PACKAGE) $VERSION$TIMESTAMP
+
+Copyright (C) 2008 Free Software Foundation, Inc.
+This is free software; see the source for copying conditions. There is NO
+warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE."
exit $?
;;
*.class) xform=class ;;
*.cpp) xform=cpp ;;
*.cxx) xform=cxx ;;
- *.f90) xform=f90 ;;
+ *.[fF][09]?) xform=[fF][09]. ;;
*.for) xform=for ;;
*.java) xform=java ;;
+ *.obj) xform=obj ;;
+ *.sx) xform=sx ;;
esac
libobj=`$echo "X$libobj" | $Xsed -e "s/\.$xform$/.lo/"`
$run $rm "$lobj" "$output_obj"
$show "$command"
- if $run eval "$command"; then :
+ if $run eval $lt_env "$command"; then :
else
test -n "$output_obj" && $run $rm $removelist
exit $EXIT_FAILURE
command="$command$suppress_output"
$run $rm "$obj" "$output_obj"
$show "$command"
- if $run eval "$command"; then :
+ if $run eval $lt_env "$command"; then :
else
$run $rm $removelist
exit $EXIT_FAILURE
thread_safe=no
vinfo=
vinfo_number=no
+ single_module="${wl}-single_module"
func_infer_tag $base_compile
for arg
do
case $arg in
- -all-static | -static)
- if test "X$arg" = "X-all-static"; then
+ -all-static | -static | -static-libtool-libs)
+ case $arg in
+ -all-static)
if test "$build_libtool_libs" = yes && test -z "$link_static_flag"; then
$echo "$modename: warning: complete static linking is impossible in this configuration" 1>&2
fi
dlopen_self=$dlopen_self_static
fi
prefer_static_libs=yes
- else
+ ;;
+ -static)
if test -z "$pic_flag" && test -n "$link_static_flag"; then
dlopen_self=$dlopen_self_static
fi
prefer_static_libs=built
- fi
+ ;;
+ -static-libtool-libs)
+ if test -z "$pic_flag" && test -n "$link_static_flag"; then
+ dlopen_self=$dlopen_self_static
+ fi
+ prefer_static_libs=yes
+ ;;
+ esac
build_libtool_libs=no
build_old_libs=yes
break
continue
;;
- -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe)
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
compiler_flags="$compiler_flags $arg"
compile_command="$compile_command $arg"
finalize_command="$finalize_command $arg"
continue
;;
+ -multi_module)
+ single_module="${wl}-multi_module"
+ continue
+ ;;
+
-module)
module=yes
continue
# -m* pass through architecture-specific compiler args for GCC
# -m*, -t[45]*, -txscale* pass through architecture-specific
# compiler args for GCC
- # -pg pass through profiling flag for GCC
+ # -p, -pg, --coverage, -fprofile-* pass through profiling flag for GCC
+ # -F/path gives path to uninstalled frameworks, gcc on darwin
# @file GCC response files
- -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*|-pg| \
- -t[45]*|-txscale*|@*)
+ -64|-mips[0-9]|-r[0-9][0-9]*|-xarch=*|-xtarget=*|+DA*|+DD*|-q*|-m*| \
+ -t[45]*|-txscale*|-p|-pg|--coverage|-fprofile-*|-F*|@*)
# Unknown arguments in both finalize_command and compile_command need
# to be aesthetically quoted because they are evaled later.
-no-install)
case $host in
- *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2*)
+ *-*-cygwin* | *-*-mingw* | *-*-pw32* | *-*-os2* | *-*-darwin*)
# The PATH hackery in wrapper scripts is required on Windows
- # in order for the loader to find any dlls it needs.
+ # and Darwin in order for the loader to find any dlls it needs.
$echo "$modename: warning: \`-no-install' is ignored for $host" 1>&2
$echo "$modename: warning: assuming \`-no-fast-install' instead" 1>&2
fast_install=no
continue
;;
- -static)
+ -static | -static-libtool-libs)
# The effects of -static are defined in a previous loop.
# We used to do the same as -all-static on platforms that
# didn't have a PIC flag, but the assumption that the effects
case $pass in
dlopen) libs="$dlfiles" ;;
dlpreopen) libs="$dlprefiles" ;;
- link)
- libs="$deplibs %DEPLIBS%"
- test "X$link_all_deplibs" != Xno && libs="$libs $dependency_libs"
- ;;
+ link) libs="$deplibs %DEPLIBS% $dependency_libs" ;;
esac
fi
if test "$pass" = dlopen; then
lib=
found=no
case $deplib in
- -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe)
+ -mt|-mthreads|-kthread|-Kthread|-pthread|-pthreads|--thread-safe|-threads)
if test "$linkmode,$pass" = "prog,link"; then
compile_deplibs="$deplib $compile_deplibs"
finalize_deplibs="$deplib $finalize_deplibs"
continue
fi
name=`$echo "X$deplib" | $Xsed -e 's/^-l//'`
- for searchdir in $newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path; do
+ if test "$linkmode" = lib; then
+ searchdirs="$newlib_search_path $lib_search_path $compiler_lib_search_dirs $sys_lib_search_path $shlib_search_path"
+ else
+ searchdirs="$newlib_search_path $lib_search_path $sys_lib_search_path $shlib_search_path"
+ fi
+ for searchdir in $searchdirs; do
for search_ext in .la $std_shrext .so .a; do
# Search the libtool library
lib="$searchdir/lib${name}${search_ext}"
if test "$linkmode,$pass" = "prog,link"; then
if test -n "$library_names" &&
- { test "$prefer_static_libs" = no || test -z "$old_library"; }; then
+ { { test "$prefer_static_libs" = no ||
+ test "$prefer_static_libs,$installed" = "built,yes"; } ||
+ test -z "$old_library"; }; then
# We need to hardcode the library path
if test -n "$shlibpath_var" && test -z "$avoidtemprpath" ; then
# Make sure the rpath contains only unique directories.
# we do not want to link against static libs,
# but need to link against shared
eval deplibrary_names=`${SED} -n -e 's/^library_names=\(.*\)$/\1/p' $deplib`
+ eval deplibdir=`${SED} -n -e 's/^libdir=\(.*\)$/\1/p' $deplib`
if test -n "$deplibrary_names" ; then
for tmp in $deplibrary_names ; do
depdepl=$tmp
done
- if test -f "$path/$depdepl" ; then
+ if test -f "$deplibdir/$depdepl" ; then
+ depdepl="$deplibdir/$depdepl"
+ elif test -f "$path/$depdepl" ; then
depdepl="$path/$depdepl"
+ else
+ # Can't find it, oh well...
+ depdepl=
fi
# do not add paths which are already there
case " $newlib_search_path " in
case $linkmode in
oldlib)
- if test -n "$deplibs"; then
- $echo "$modename: warning: \`-l' and \`-L' are ignored for archives" 1>&2
- fi
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ $echo "$modename: warning: \`-l' and \`-L' are ignored for archives" 1>&2 ;;
+ esac
if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
$echo "$modename: warning: \`-dlopen' is ignored for archives" 1>&2
# which has an extra 1 added just for fun
#
case $version_type in
- darwin|linux|osf|windows)
+ darwin|linux|osf|windows|none)
current=`expr $number_major + $number_minor`
age="$number_minor"
revision="$number_revision"
age="0"
;;
irix|nonstopux)
- current=`expr $number_major + $number_minor - 1`
+ current=`expr $number_major + $number_minor`
age="$number_minor"
revision="$number_minor"
- ;;
- *)
- $echo "$modename: unknown library version type \`$version_type'" 1>&2
- $echo "Fatal configuration error. See the $PACKAGE docs for more information." 1>&2
- exit $EXIT_FAILURE
+ lt_irix_increment=no
;;
esac
;;
versuffix="$major.$age.$revision"
# Darwin ld doesn't like 0 for these options...
minor_current=`expr $current + 1`
- verstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ xlcverstring="${wl}-compatibility_version ${wl}$minor_current ${wl}-current_version ${wl}$minor_current.$revision"
+ verstring="-compatibility_version $minor_current -current_version $minor_current.$revision"
;;
freebsd-aout)
;;
irix | nonstopux)
- major=`expr $current - $age + 1`
-
+ if test "X$lt_irix_increment" = "Xno"; then
+ major=`expr $current - $age`
+ else
+ major=`expr $current - $age + 1`
+ fi
case $version_type in
nonstopux) verstring_prefix=nonstopux ;;
*) verstring_prefix=sgi ;;
fi
# Eliminate all temporary directories.
- for path in $notinst_path; do
- lib_search_path=`$echo "$lib_search_path " | ${SED} -e "s% $path % %g"`
- deplibs=`$echo "$deplibs " | ${SED} -e "s% -L$path % %g"`
- dependency_libs=`$echo "$dependency_libs " | ${SED} -e "s% -L$path % %g"`
- done
+ #for path in $notinst_path; do
+ # lib_search_path=`$echo "$lib_search_path " | ${SED} -e "s% $path % %g"`
+ # deplibs=`$echo "$deplibs " | ${SED} -e "s% -L$path % %g"`
+ # dependency_libs=`$echo "$dependency_libs " | ${SED} -e "s% -L$path % %g"`
+ #done
if test -n "$xrpath"; then
# If the user specified any rpath flags, then add them.
int main() { return 0; }
EOF
$rm conftest
- $LTCC $LTCFLAGS -o conftest conftest.c $deplibs
- if test "$?" -eq 0 ; then
+ if $LTCC $LTCFLAGS -o conftest conftest.c $deplibs; then
ldd_output=`ldd conftest`
for i in $deplibs; do
name=`expr $i : '-l\(.*\)'`
# If $name is empty we are operating on a -L argument.
- if test "$name" != "" && test "$name" -ne "0"; then
+ if test "$name" != "" && test "$name" != "0"; then
if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
case " $predeps $postdeps " in
*" $i "*)
# If $name is empty we are operating on a -L argument.
if test "$name" != "" && test "$name" != "0"; then
$rm conftest
- $LTCC $LTCFLAGS -o conftest conftest.c $i
- # Did it work?
- if test "$?" -eq 0 ; then
+ if $LTCC $LTCFLAGS -o conftest conftest.c $i; then
ldd_output=`ldd conftest`
if test "X$allow_libtool_libs_with_static_runtimes" = "Xyes" ; then
case " $predeps $postdeps " in
droppeddeps=yes
$echo
$echo "*** Warning! Library $i is needed by this library but I was not able to"
- $echo "*** make it link in! You will probably need to install it or some"
+ $echo "*** make it link in! You will probably need to install it or some"
$echo "*** library that it depends on before this library will be fully"
$echo "*** functional. Installing it before continuing would be even better."
fi
test -n "$hardcode_libdirs"; then
libdir="$hardcode_libdirs"
if test -n "$hardcode_libdir_flag_spec_ld"; then
- eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\"
+ case $archive_cmds in
+ *\$LD*) eval dep_rpath=\"$hardcode_libdir_flag_spec_ld\" ;;
+ *) eval dep_rpath=\"$hardcode_libdir_flag_spec\" ;;
+ esac
else
eval dep_rpath=\"$hardcode_libdir_flag_spec\"
fi
;;
obj)
- if test -n "$deplibs"; then
- $echo "$modename: warning: \`-l' and \`-L' are ignored for objects" 1>&2
- fi
+ case " $deplibs" in
+ *\ -l* | *\ -L*)
+ $echo "$modename: warning: \`-l' and \`-L' are ignored for objects" 1>&2 ;;
+ esac
if test -n "$dlfiles$dlprefiles" || test "$dlself" != no; then
$echo "$modename: warning: \`-dlopen' is ignored for objects" 1>&2
reload_conv_objs=
gentop=
# reload_cmds runs $LD directly, so let us get rid of
- # -Wl from whole_archive_flag_spec
+ # -Wl from whole_archive_flag_spec and hope we can get by with
+ # turning comma into space..
wl=
if test -n "$convenience"; then
if test -n "$whole_archive_flag_spec"; then
- eval reload_conv_objs=\"\$reload_objs $whole_archive_flag_spec\"
+ eval tmp_whole_archive_flags=\"$whole_archive_flag_spec\"
+ reload_conv_objs=$reload_objs\ `$echo "X$tmp_whole_archive_flags" | $Xsed -e 's|,| |g'`
else
gentop="$output_objdir/${obj}x"
generated="$generated $gentop"
case $host in
*cygwin* | *mingw* )
if test -f "$output_objdir/${outputname}.def" ; then
- compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%"`
- finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%"`
+ compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%" | $NL2SP`
+ finalize_command=`$echo "X$finalize_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}.def $output_objdir/${outputname}S.${objext}%" | $NL2SP`
else
- compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
- finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+ compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%" | $NL2SP`
+ finalize_command=`$echo "X$finalize_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%" | $NL2SP`
fi
;;
* )
- compile_command=`$echo "X$compile_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
- finalize_command=`$echo "X$finalize_command" | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%"`
+ compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%" | $NL2SP`
+ finalize_command=`$echo "X$finalize_command" | $SP2NL | $Xsed -e "s%@SYMFILE@%$output_objdir/${outputname}S.${objext}%" | $NL2SP`
;;
esac
;;
# really was required.
# Nullify the symbol file.
- compile_command=`$echo "X$compile_command" | $Xsed -e "s% @SYMFILE@%%"`
- finalize_command=`$echo "X$finalize_command" | $Xsed -e "s% @SYMFILE@%%"`
+ compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e "s% @SYMFILE@%%" | $NL2SP`
+ finalize_command=`$echo "X$finalize_command" | $SP2NL | $Xsed -e "s% @SYMFILE@%%" | $NL2SP`
fi
if test "$need_relink" = no || test "$build_libtool_libs" != yes; then
# Replace the output file specification.
- compile_command=`$echo "X$compile_command" | $Xsed -e 's%@OUTPUT@%'"$output"'%g'`
+ compile_command=`$echo "X$compile_command" | $SP2NL | $Xsed -e 's%@OUTPUT@%'"$output"'%g' | $NL2SP`
link_command="$compile_command$compile_rpath"
# We have no uninstalled library dependencies, so finalize right now.
if test "$fast_install" != no; then
link_command="$finalize_var$compile_command$finalize_rpath"
if test "$fast_install" = yes; then
- relink_command=`$echo "X$compile_var$compile_command$compile_rpath" | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g'`
+ relink_command=`$echo "X$compile_var$compile_command$compile_rpath" | $SP2NL | $Xsed -e 's%@OUTPUT@%\$progdir/\$file%g' | $NL2SP`
else
# fast_install is set to needless
relink_command=
fi
done
relink_command="(cd `pwd`; $relink_command)"
- relink_command=`$echo "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ relink_command=`$echo "X$relink_command" | $SP2NL | $Xsed -e "$sed_quote_subst" | $NL2SP`
fi
# Quote $echo for shipping.
Xsed='${SED} -e 1s/^X//'
sed_quote_subst='$sed_quote_subst'
+# Be Bourne compatible (taken from Autoconf:_AS_BOURNE_COMPATIBLE).
+if test -n \"\${ZSH_VERSION+set}\" && (emulate sh) >/dev/null 2>&1; then
+ emulate sh
+ NULLCMD=:
+ # Zsh 3.x and 4.x performs word splitting on \${1+\"\$@\"}, which
+ # is contrary to our usage. Disable this feature.
+ alias -g '\${1+\"\$@\"}'='\"\$@\"'
+ setopt NO_GLOB_SUBST
+else
+ case \`(set -o) 2>/dev/null\` in *posix*) set -o posix;; esac
+fi
+BIN_SH=xpg4; export BIN_SH # for Tru64
+DUALCASE=1; export DUALCASE # for MKS sh
+
# The HP-UX ksh and POSIX shell print the target directory to stdout
# if CDPATH is set.
(unset CDPATH) >/dev/null 2>&1 && unset CDPATH
;;
esac
$echo >> $output "\
- \$echo \"\$0: cannot exec \$program \${1+\"\$@\"}\"
+ \$echo \"\$0: cannot exec \$program \$*\"
exit $EXIT_FAILURE
fi
else
done
# Quote the link command for shipping.
relink_command="(cd `pwd`; $SHELL $progpath $preserve_args --mode=relink $libtool_args @inst_prefix_dir@)"
- relink_command=`$echo "X$relink_command" | $Xsed -e "$sed_quote_subst"`
+ relink_command=`$echo "X$relink_command" | $SP2NL | $Xsed -e "$sed_quote_subst" | $NL2SP`
if test "$hardcode_automatic" = yes ; then
relink_command=
fi
if test -n "$inst_prefix_dir"; then
# Stick the inst_prefix_dir data into the link command.
- relink_command=`$echo "$relink_command" | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%"`
+ relink_command=`$echo "$relink_command" | $SP2NL | $SED "s%@inst_prefix_dir@%-inst-prefix-dir $inst_prefix_dir%" | $NL2SP`
else
- relink_command=`$echo "$relink_command" | $SED "s%@inst_prefix_dir@%%"`
+ relink_command=`$echo "$relink_command" | $SP2NL | $SED "s%@inst_prefix_dir@%%" | $NL2SP`
fi
$echo "$modename: warning: relinking \`$file'" 1>&2
file=`$echo "X$file$stripped_ext" | $Xsed -e 's%^.*/%%'`
outputname="$tmpdir/$file"
# Replace the output file specification.
- relink_command=`$echo "X$relink_command" | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g'`
+ relink_command=`$echo "X$relink_command" | $SP2NL | $Xsed -e 's%@OUTPUT@%'"$outputname"'%g' | $NL2SP`
$show "$relink_command"
if $run eval "$relink_command"; then :
if test -f "$dir/$objdir/$dlname"; then
dir="$dir/$objdir"
else
- $echo "$modename: cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" 1>&2
- exit $EXIT_FAILURE
+ if test ! -f "$dir/$dlname"; then
+ $echo "$modename: cannot find \`$dlname' in \`$dir' or \`$dir/$objdir'" 1>&2
+ exit $EXIT_FAILURE
+ fi
fi
;;
fi
# Restore saved environment variables
- if test "${save_LC_ALL+set}" = set; then
- LC_ALL="$save_LC_ALL"; export LC_ALL
- fi
- if test "${save_LANG+set}" = set; then
- LANG="$save_LANG"; export LANG
- fi
+ for lt_var in LANG LANGUAGE LC_ALL LC_CTYPE LC_COLLATE LC_MESSAGES
+ do
+ eval "if test \"\${save_$lt_var+set}\" = set; then
+ $lt_var=\$save_$lt_var; export $lt_var
+ fi"
+ done
# Now prepare to actually exec the command.
exec_cmd="\$cmd$args"
-dlpreopen FILE link in FILE and add its symbols to lt_preloaded_symbols
-export-dynamic allow symbols from OUTPUT-FILE to be resolved with dlsym(3)
-export-symbols SYMFILE
- try to export only the symbols listed in SYMFILE
+ try to export only the symbols listed in SYMFILE
-export-symbols-regex REGEX
- try to export only the symbols matching REGEX
+ try to export only the symbols matching REGEX
-LLIBDIR search LIBDIR for required installed libraries
-lNAME OUTPUT-FILE requires the installed library libNAME
-module build a library that can dlopened
-release RELEASE specify package release information
-rpath LIBDIR the created library will eventually be installed in LIBDIR
-R[ ]LIBDIR add LIBDIR to the runtime path of programs and libraries
- -static do not do any dynamic linking of libtool libraries
+ -static do not do any dynamic linking of uninstalled libtool libraries
+ -static-libtool-libs
+ do not do any dynamic linking of libtool libraries
-version-info CURRENT[:REVISION[:AGE]]
- specify library version info [each variable defaults to 0]
+ specify library version info [each variable defaults to 0]
All other options (arguments beginning with \`-') are ignored.
#######################################################################
AC_PREREQ(2.50)
-AC_INIT(gromacs, 4.0_rc1, [gmx-users@gromacs.org])
+AC_INIT(gromacs, 4.0, [gmx-users@gromacs.org])
AC_CONFIG_SRCDIR(src/gmxlib/3dview.c)
AC_CONFIG_AUX_DIR(config)
AC_CANONICAL_HOST
AM_CONFIG_HEADER(src/config.h)
dnl This is the version info according to the libtool versioning system.
dnl It does *not* correspond to the release number.
-SHARED_VERSION_INFO="4:0:0"
+SHARED_VERSION_INFO="5:0:0"
AC_SUBST(SHARED_VERSION_INFO)
-# MPI builds on aix break with shared libs, so they are disabled by default.
AC_DISABLE_SHARED
+
#######################################################################
# Simple options and makefile variables
#######################################################################
AC_DEFINE_UNQUOTED(GMX_CHECK_MPI_ENV,"$enable_mpi_environment",[If defined, only start MPI runs when this variable is set])
fi
+AC_ARG_ENABLE(apple_64bit,
+ [AC_HELP_STRING([--enable-apple-64bit],
+ [Build 64bit binaries for newer Macs])],,enable_apple_64bit=no)
+
+
### IA32 assembly code
AC_ARG_ENABLE(ia32_3dnow,
[AC_HELP_STRING([--disable-ia32-3dnow],
[Don't build 3DNow! assembly loops on ia32])],,enable_ia32_3dnow=yes)
case "${host_cpu}" in
- i?86) ;;
+ i?86)
+ if test "$enable_apple_64bit" = "yes"; then
+ enable_ia32_3dnow=no;
+ fi
+ ;;
*) enable_ia32_3dnow=no ;;
esac
AC_ARG_ENABLE(ia32_sse,
[AC_HELP_STRING([--disable-ia32-sse],
[Don't build SSE/SSE2 assembly loops on ia32])],,enable_ia32_sse=yes)
-case "${host_cpu}" in
- i?86) ;;
+case "${host_cpu}-${host_vendor}" in
+ i?86-apple)
+ if test "$enable_apple_64bit" = "yes"; then
+ enable_ia32_sse=no;
+ fi
+ ;;
+ i?86-*) ;;
*) enable_ia32_sse=no ;;
esac
AC_ARG_ENABLE(x86_64_sse,
[AC_HELP_STRING([--disable-x86-64-sse],
[Don't build SSE assembly loops on X86_64])],,enable_x86_64_sse=yes)
-case "${host_cpu}" in
- x86_64 | amd64) ;;
+case "${host_cpu}-${host_vendor}" in
+ x86_64-* | amd64-*) ;;
+ i?86-apple)
+ if test "$enable_apple_64bit" != "yes"; then
+ enable_x86_64_sse=no;
+ fi
+ ;;
*) enable_x86_64_sse=no ;;
esac
fi
+
### ia64 assembly code
AC_ARG_ENABLE(ia64_asm,
[AC_HELP_STRING([--disable-ia64-asm],
#
fi
-# Class Library For Numbers Module
-AC_ARG_WITH(cln,
- [ --with-cln Class Library For Numbers Module],,with_cln=no)
-
-######
-if test "$with_cln" = "yes"; then
- AC_LANG_PUSH([C++])
-# AC_REQUIRE([AC_PROG_CXX])
-# AC_REQUIRE([_LT_AC_PROG_CXXCPP])
- AC_CHECK_HEADERS([cln/cln.h],
-# header found, check for libraries
- AC_CHECK_LIB(cln,main))
- AC_LANG_POP([C++])
-fi
AC_ARG_WITH(xml,
[ --without-xml do not link to the xml2 library, disallows the use of certain file formats],,with_xml=yes)
ret
EOF
fi
- if AC_TRY_COMMAND($CC -c conftestasm.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftestasm.s); then
if test -f conftestasm.o; then
AC_MSG_RESULT([yes])
else
emms
ret
EOF
- if AC_TRY_COMMAND($CC -c conftest.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftest.s); then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
emms
ret
EOF
- if AC_TRY_COMMAND($CC -c conftest.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftest.s); then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
emms
ret
EOF
- if AC_TRY_COMMAND($CC -c conftest.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftest.s); then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
emms
ret
EOF
- if AC_TRY_COMMAND($CC -c conftest.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftest.s); then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
emms
ret
EOF
- if AC_TRY_COMMAND($CC -c conftest.s); then
+ if AC_TRY_COMMAND($CC $CFLAGS -c conftest.s); then
AC_MSG_RESULT([yes])
else
AC_MSG_RESULT([no])
echo " installed you can issue make mdrun; make install-mdrun."
fi
+if test "$host_vendor" = "apple" -a "$enable_apple_64bit" = "no"; then
+ echo ""
+ echo "* Did you know that you can compile a 64-bit version of Gromacs to improve"
+ echo " performance on recent Intel Macs? You need to install a 64-bit version"
+ echo " of FFTW first (add -m64 to CFLAGS, or download it from the Gromacs site)"
+ echo " after which you can simply specify --enable-apple-64bit to this script."
+fi
+
+if test "$enable_shared" = "no"; then
+ echo ""
+ echo "* On most platforms you can save 10X space with dynamic libraries, although"
+ echo " the binaries might be less portable. Why not try --enable-shared ?"
+fi
+
echo ""
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _gmx_ana_h
#define _gmx_ana_h
-/* -*- mode: c; tab-width: 4; indent-tabs-mode: m; c-basic-offset: 4 -*-
- *
+/*
* $Id$
*
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
+/*
* This file is part of Gromacs Copyright (c) 1991-2004
* David van der Spoel, Erik Lindahl, University of Groningen.
*
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _GMX_BLAS_H_
#define _GMX_BLAS_H_
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifndef _GMX_LAPACK_H_
#define _GMX_LAPACK_H_
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _GMX_RANDOM_H_
#define _GMX_RANDOM_H_
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _gmx_wallcycle_h
#define _gmx_wallcycle_h
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
+
/* define USE_MPE if you want MPE logging
*
* you then need to link with the appropriate libraries
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _QMMM_h
#define _QMMM_h
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifdef HAVE_CONFIG_H
#include<config.h>
#endif
* else if bMass=TRUE, read the masses into top.atoms from the mass database.
*/
+void
+tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols);
+
#ifdef CPLUSPLUS
}
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
real y2;
#endif
- lu = __frsqrte(dble(x));
+ lu = __frsqrte(double(x));
y=(half*lu*(three-((x*lu)*lu)));
man_MANS = \
anadock.1 g_cluster.1 g_filter.1 g_potential.1 \
- g_velacc.1 ngmx.1 cdist.1 g_clustsize.1 \
+ g_velacc.1 ngmx.1 g_clustsize.1 g_vanhove.1 \
g_gyrate.1 g_rama.1 g_wham.1 pdb2gmx.1 \
- disco.1 g_confrms.1 g_h2order.1 g_rdf.1 \
+ g_confrms.1 g_h2order.1 g_rdf.1 genrestr.1 \
genbox.1 protonate.1 do_dssp.1 g_covar.1 \
g_hbond.1 g_rms.1 genconf.1 tpbconv.1 \
editconf.1 g_density.1 g_helix.1 g_rmsdist.1 \
genion.1 trjcat.1 eneconv.1 g_dielectric.1 \
- g_lie.1 g_rmsf.1 genpr.1 trjconv.1 \
- ffscan.1 g_dih.1 g_mdmat.1 g_rotacf.1 \
+ g_lie.1 g_rmsf.1 trjconv.1 g_helixorient.1 \
+ g_dih.1 g_mdmat.1 g_rotacf.1 sigeps.1 \
gmxcheck.1 trjorder.1 g_anaeig.1 g_dipoles.1 \
g_mindist.1 g_saltbr.1 gmxdump.1 wheel.1 \
g_analyze.1 g_disre.1 g_morph.1 g_sas.1 \
make_ndx.1 xrama.1 g_bundle.1 g_enemat.1 \
g_nmens.1 g_tcaf.1 mdrun.1 g_chi.1 \
g_energy.1 g_order.1 g_traj.1 mk_angndx.1 \
- g_densmap.1 g_sham.1 make_edi.1
+ g_densmap.1 g_sham.1 make_edi.1 g_spol.1 \
+ g_spatial.1 g_sdf.1 g_rama.1 g_principal.1 \
+ g_polystat.1 g_nmtraj.1 g_current.1
EXTRA_DIST = ${man_MANS}
\ No newline at end of file
-.TH anadock 1 "Mon 29 Aug 2005"
+.TH anadock 1 "Mon 22 Sep 2008"
.SH NAME
anadock
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3anadock\fP
.BI "-f" " eiwit.pdb "
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]free" " no"
+.BI "-[no]free" "no "
Use Free energy estimate from autodock for sorting the classes
-.BI "-[no]rms" " yes"
+.BI "-[no]rms" "yes "
Cluster on RMS or distance
-.BI "-cutoff" " real" " 0.2"
+.BI "-cutoff" " real" " 0.2 "
Maximum RMSD/distance for belonging to the same cluster
-.TH do_dssp 1 "Mon 29 Aug 2005"
+.TH do_dssp 1 "Mon 22 Sep 2008"
.SH NAME
do_dssp
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3do_dssp\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-sss" " string" " HEBT"
Secondary structures for structure count
-\- The program is very slow
-
-.TH editconf 1 "Mon 29 Aug 2005"
+.TH editconf 1 "Mon 22 Sep 2008"
.SH NAME
editconf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3editconf\fP
.BI "-f" " conf.gro "
Option
.B -bt
determines the box type:
-.B tric
+.B triclinic
is a
triclinic box,
.B cubic
-is a cubic box,
+is a rectangular box with all sides equal
+
.B dodecahedron
-is
-a rhombic dodecahedron and
+represents a rhombic dodecahedron and
.B octahedron
is a truncated octahedron.
The last two are special cases of a triclinic box.
.B -box
requires only
one value for a cubic box, dodecahedron and a truncated octahedron.
+
+
+
With
.B -d
-and
-.B tric
-the size of the system in the x, y
+and a
+.B triclinic
+box the size of the system in the x, y
and z directions is used. With
.B -d
and
.B dodecahedron
or
.B octahedron
-the diameter of the system
-is used, which is the largest distance between two atoms.
+boxes, the dimensions are set
+to the diameter of the system (largest distance between atoms) plus twice
+the specified distance.
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-mead" " mead.pqr"
.B Output, Opt.
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]ndef" " no"
+.BI "-[no]ndef" "no "
Choose output from default index groups
-.BI "-bt" " enum" " tric"
+.BI "-bt" " enum" " triclinic"
Box type for -box and -d:
-.B tric
+.B triclinic
,
.B cubic
,
.BI "-angles" " vector" " 90 90 90"
Angles between the box vectors (bc,ac,ab)
-.BI "-d" " real" " 0"
+.BI "-d" " real" " 0 "
Distance between the solute and the box
-.BI "-[no]c" " no"
+.BI "-[no]c" "no "
Center molecule in box (implied by -box and -d)
.BI "-center" " vector" " 0 0 0"
.BI "-rotate" " vector" " 0 0 0"
Rotation around the X, Y and Z axes in degrees
-.BI "-[no]princ" " no"
+.BI "-[no]princ" "no "
Orient molecule(s) along their principal axes
.BI "-scale" " vector" " 1 1 1"
Scaling factor
-.BI "-density" " real" " 1000"
+.BI "-density" " real" " 1000 "
Density (g/l) of the output box achieved by scaling
-.BI "-[no]vol" " yes"
+.BI "-[no]vol" "yes "
Compute and print volume of the box
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Remove the periodicity (make molecule whole again)
-.BI "-[no]grasp" " no"
+.BI "-[no]grasp" "no "
Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field
-.BI "-rvdw" " real" " 0.12"
+.BI "-rvdw" " real" " 0.12 "
Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file
-.BI "-sig56" " real" " 0"
+.BI "-sig56" " real" " 0 "
Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2
-.BI "-[no]vdwread" " no"
+.BI "-[no]vdwread" "no "
Read the Van der Waals radii from the file vdwradii.dat rather than computing the radii based on the force field
-.BI "-[no]atom" " no"
+.BI "-[no]atom" "no "
Force B-factor attachment per atom
-.BI "-[no]legend" " no"
+.BI "-[no]legend" "no "
Make B-factor legend
.BI "-label" " string" " A"
Add chain label for all residues
+.SH KNOWN PROBLEMS
\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
-.TH eneconv 1 "Mon 29 Aug 2005"
+.TH eneconv 1 "Mon 22 Sep 2008"
.SH NAME
eneconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3eneconv\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input, Mult.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-o" " fixed.edr"
.B Output
- Generic energy: edr ene
+ Energy file: edr ene
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to use
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to use
-.BI "-dt" " real" " 0"
+.BI "-dt" " real" " 0 "
Only write out frame when t MOD dt = offset
-.BI "-offset" " real" " 0"
+.BI "-offset" " real" " 0 "
Time offset for -dt option
-.BI "-[no]settime" " no"
+.BI "-[no]settime" "no "
Change starting time interactively
-.BI "-[no]sort" " yes"
+.BI "-[no]sort" "yes "
Sort energy files (not frames)
-.BI "-scalefac" " real" " 1"
+.BI "-scalefac" " real" " 1 "
Multiply energy component by this factor
-.BI "-[no]error" " yes"
+.BI "-[no]error" "yes "
Stop on errors in the file
+.SH KNOWN PROBLEMS
\- When combining trajectories the sigma and E2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
-.TH g_anaeig 1 "Mon 29 Aug 2005"
+.TH g_anaeig 1 "Mon 22 Sep 2008"
.SH NAME
g_anaeig
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "-v" " eigenvec.trr "
.BI "-max" " real "
.BI "-nframes" " int "
.BI "-[no]split" ""
+.BI "-[no]entropy" ""
+.BI "-temp" " real "
+.BI "-nevskip" " int "
.SH DESCRIPTION
.B g_anaeig
root of the fluctuations. The normalized overlap is the most useful
number, it is 1 for identical matrices and 0 when the sampled
subspaces are orthogonal.
+
+
+When the
+.B -entropy
+flag is given an entropy estimate will be
+computed based on the Quasiharmonic approach and based on
+Schlitter's formula.
.SH FILES
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-v2" " eigenvec2.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-3d" " 3dproj.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-filt" " filtered.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-extr" " extreme.pdb"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-over" " overlap.xvg"
.B Output, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-first" " int" " 1"
.BI "-skip" " int" " 1"
Only analyse every nr-th frame
-.BI "-max" " real" " 0"
+.BI "-max" " real" " 0 "
Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes
.BI "-nframes" " int" " 2"
Number of frames for the extremes output
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split eigenvector projections where time is zero
+.BI "-[no]entropy" "no "
+ Compute entropy according to the Quasiharmonic formula or Schlitter's method.
+
+.BI "-temp" " real" " 298.15"
+ Temperature for entropy calculations
+
+.BI "-nevskip" " int" " 6"
+ Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy.
+
-.TH g_analyze 1 "Mon 29 Aug 2005"
+.TH g_analyze 1 "Mon 22 Sep 2008"
.SH NAME
g_analyze
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_analyze\fP
.BI "-f" " graph.xvg "
.BI "-[no]integrate" ""
.BI "-aver_start" " real "
.BI "-[no]xydy" ""
+.BI "-[no]regression" ""
+.BI "-[no]luzar" ""
+.BI "-temp" " real "
+.BI "-fitstart" " real "
+.BI "-smooth" " real "
.BI "-filter" " real "
.BI "-[no]power" ""
.BI "-[no]subav" ""
.B -cc
plots the resemblance of set i with a cosine of
i/2 periods. The formula is:
-2 (int0-T y(t) cos(pi t/i) dt)2 / int0-T y(t) y(t) dt
+2 (int0-T y(t) cos(i pi t) dt)2 / int0-T y(t) y(t) dt
This is useful for principal components obtained from covariance
analysis, since the principal components of random diffusion are
of 0.79 and 0.33 respectively.
+Option
+.B -g
+fits the data to the function given with option
+
+.B -fitfn
+.
+
+
Option
.B -power
fits the data to b ta, which is accomplished
by fitting to a t + b on log-log scale. All points after the first
zero or negative value are ignored.
+
+Option
+.B -luzar
+performs a Luzar & Chandler kinetics analysis
+on output from
+.B g_hbond
+. The input file can be taken directly
+from
+.B g_hbond -ac
+, and then the same result should be produced.
.SH FILES
.BI "-f" " graph.xvg"
.B Input
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]time" " yes"
+.BI "-[no]time" "yes "
Expect a time in the input
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to read from set
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to read from set
.BI "-n" " int" " 1"
Read sets seperated by &
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use the derivative
-.BI "-bw" " real" " 0.1"
+.BI "-bw" " real" " 0.1 "
Binwidth for the distribution
.BI "-errbar" " enum" " none"
.B 90
-.BI "-[no]integrate" " no"
+.BI "-[no]integrate" "no "
Integrate data function(s) numerically using trapezium rule
-.BI "-aver_start" " real" " 0"
+.BI "-aver_start" " real" " 0 "
Start averaging the integral from here
-.BI "-[no]xydy" " no"
+.BI "-[no]xydy" "no "
Interpret second data set as error in the y values for integrating
-.BI "-filter" " real" " 0"
+.BI "-[no]regression" "no "
+ Perform a linear regression analysis on the data
+
+.BI "-[no]luzar" "no "
+ Do a Luzar and Chandler analysis on a correlation function and related as produced by g_hbond. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t).
+
+.BI "-temp" " real" " 298.15"
+ Temperature for the Luzar hydrogen bonding kinetics analysis
+
+.BI "-fitstart" " real" " 1 "
+ Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
+
+.BI "-smooth" " real" " -1 "
+ If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
+
+.BI "-filter" " real" " 0 "
Print the high-frequency fluctuation after filtering with a cosine filter of length
-.BI "-[no]power" " no"
+.BI "-[no]power" "no "
Fit data to: b ta
-.BI "-[no]subav" " yes"
+.BI "-[no]subav" "yes "
Subtract the average before autocorrelating
-.BI "-[no]oneacf" " no"
+.BI "-[no]oneacf" "no "
Calculate one ACF over all sets
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_angle 1 "Mon 29 Aug 2005"
+.TH g_angle 1 "Mon 22 Sep 2008"
.SH NAME
g_angle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_angle\fP
.BI "-f" " traj.xtc "
-.BI "-s" " topol.tpr "
.BI "-n" " angle.ndx "
.BI "-od" " angdist.xvg "
.BI "-ov" " angaver.xvg "
.BI "-type" " enum "
.BI "-[no]all" ""
.BI "-binwidth" " real "
+.BI "-[no]periodic" ""
.BI "-[no]chandler" ""
.BI "-[no]avercorr" ""
.BI "-acflen" " int "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
-
-.BI "-s" " topol.tpr"
-.B Input
- Generic run input: tpr tpb tpa xml
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " angle.ndx"
.B Input
Trajectory in portable xdr format
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-type" " enum" " angle"
.B ryckaert-bellemans
-.BI "-[no]all" " no"
+.BI "-[no]all" "no "
Plot all angles separately in the averages file, in the order of appearance in the index file.
-.BI "-binwidth" " real" " 1"
+.BI "-binwidth" " real" " 1 "
binwidth (degrees) for calculating the distribution
-.BI "-[no]chandler" " no"
+.BI "-[no]periodic" "yes "
+ Print dihedral angles modulo 360 degrees
+
+.BI "-[no]chandler" "no "
Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi -60 || phi 60.
-.BI "-[no]avercorr" " no"
+.BI "-[no]avercorr" "no "
Average the correlation functions for the individual angles/dihedrals
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
\- Counting transitions only works for dihedrals with multiplicity 3
-.TH g_bond 1 "Mon 29 Aug 2005"
+.TH g_bond 1 "Mon 22 Sep 2008"
.SH NAME
g_bond
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_bond\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-o" " bonds.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-blen" " real" " -1"
+.BI "-blen" " real" " -1 "
Bond length. By default length of first bond
-.BI "-tol" " real" " 0.1"
+.BI "-tol" " real" " 0.1 "
Half width of distribution as fraction of blen
-.BI "-[no]aver" " yes"
+.BI "-[no]aver" "yes "
Average bond length distributions
-.BI "-[no]averdist" " yes"
+.BI "-[no]averdist" "yes "
Average distances (turns on -d)
+.SH KNOWN PROBLEMS
\- It should be possible to get bond information from the topology.
-.TH g_bundle 1 "Mon 29 Aug 2005"
+.TH g_bundle 1 "Mon 22 Sep 2008"
.SH NAME
g_bundle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_bundle\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Protein data bank file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-na" " int" " 0"
Number of axes
-.BI "-[no]z" " no"
+.BI "-[no]z" "no "
Use the Z-axis as reference iso the average axis
-.TH g_chi 1 "Mon 29 Aug 2005"
+.TH g_chi 1 "Mon 22 Sep 2008"
.SH NAME
g_chi
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_chi\fP
.BI "-s" " conf.gro "
.BI "-[no]omega" ""
.BI "-[no]rama" ""
.BI "-[no]viol" ""
+.BI "-[no]periodic" ""
.BI "-[no]all" ""
.BI "-[no]rad" ""
.BI "-[no]shift" ""
.SH FILES
.BI "-s" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " order.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-r0" " int" " 1"
starting residue
-.BI "-[no]phi" " no"
+.BI "-[no]phi" "no "
Output for Phi dihedral angles
-.BI "-[no]psi" " no"
+.BI "-[no]psi" "no "
Output for Psi dihedral angles
-.BI "-[no]omega" " no"
+.BI "-[no]omega" "no "
Output for Omega dihedrals (peptide bonds)
-.BI "-[no]rama" " no"
+.BI "-[no]rama" "no "
Generate Phi/Psi and Chi1/Chi2 ramachandran plots
-.BI "-[no]viol" " no"
+.BI "-[no]viol" "no "
Write a file that gives 0 or 1 for violated Ramachandran angles
-.BI "-[no]all" " no"
+.BI "-[no]periodic" "yes "
+ Print dihedral angles modulo 360 degrees
+
+.BI "-[no]all" "no "
Output separate files for every dihedral.
-.BI "-[no]rad" " no"
+.BI "-[no]rad" "no "
in angle vs time files, use radians rather than degrees.
-.BI "-[no]shift" " no"
+.BI "-[no]shift" "no "
Compute chemical shifts from Phi/Psi angles
.BI "-binwidth" " int" " 1"
bin width for histograms (degrees)
-.BI "-core_rotamer" " real" " 0.5"
+.BI "-core_rotamer" " real" " 0.5 "
only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0)
.BI "-maxchi" " enum" " 0"
.B 6
-.BI "-[no]normhisto" " yes"
+.BI "-[no]normhisto" "yes "
Normalize histograms
-.BI "-[no]ramomega" " no"
+.BI "-[no]ramomega" "no "
compute average omega as a function of phi/psi and plot it in an xpm plot
-.BI "-bfact" " real" " -1"
+.BI "-bfact" " real" " -1 "
B-factor value for pdb file for atoms with no calculated dihedral order parameter
-.BI "-[no]chi_prod" " no"
+.BI "-[no]chi_prod" "no "
compute a single cumulative rotamer for each residue
-.BI "-[no]HChi" " no"
+.BI "-[no]HChi" "no "
Include dihedrals to sidechain hydrogens
-.BI "-bmax" " real" " 0"
+.BI "-bmax" " real" " 0 "
Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax = 0 means no limit.
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
\- Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
\- Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like g_rama.
-.TH g_cluster 1 "Mon 29 Aug 2005"
+.TH g_cluster 1 "Mon 22 Sep 2008"
.SH NAME
g_cluster
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_cluster\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-cl" " clusters.pdb"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]dista" " no"
+.BI "-[no]dista" "no "
Use RMSD of distances instead of RMS deviation
.BI "-nlevels" " int" " 40"
Discretize RMSD matrix in levels
-.BI "-cutoff" " real" " 0.1"
+.BI "-cutoff" " real" " 0.1 "
RMSD cut-off (nm) for two structures to be neighbor
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Use least squares fitting before RMSD calculation
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in RMSD matrix
.BI "-skip" " int" " 1"
Only analyze every nr-th frame
-.BI "-[no]av" " no"
+.BI "-[no]av" "no "
Write average iso middle structure for each cluster
.BI "-wcl" " int" " 0"
.BI "-nst" " int" " 1"
Only write all structures if more than per cluster
-.BI "-rmsmin" " real" " 0"
+.BI "-rmsmin" " real" " 0 "
minimum rms difference with rest of cluster for writing structures
.BI "-method" " enum" " linkage"
.BI "-minstruct" " int" " 1"
Minimum number of structures in cluster for coloring in the xpm file
-.BI "-[no]binary" " no"
+.BI "-[no]binary" "no "
Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
.BI "-M" " int" " 10"
.BI "-niter" " int" " 10000"
Number of iterations for MC
-.BI "-kT" " real" " 0.001"
+.BI "-kT" " real" " 0.001 "
Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)
-.TH g_clustsize 1 "Mon 29 Aug 2005"
+.TH g_clustsize 1 "Mon 22 Sep 2008"
.SH NAME
g_clustsize
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-cut" " real" " 0.35"
+.BI "-cut" " real" " 0.35 "
Largest distance (nm) to be considered in a cluster
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Cluster molecules rather than atoms (needs tpr file)
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Use periodic boundary conditions
.BI "-nskip" " int" " 0"
-.TH g_confrms 1 "Mon 29 Aug 2005"
+.TH g_confrms 1 "Mon 22 Sep 2008"
.SH NAME
g_confrms
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_confrms\fP
.BI "-f1" " conf1.gro "
.BI "-[no]pbc" ""
.BI "-[no]fit" ""
.BI "-[no]name" ""
+.BI "-[no]label" ""
.BI "-[no]bfac" ""
.SH DESCRIPTION
g_confrms computes the root mean square deviation (RMSD) of two
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " fit.pdb"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-n1" " fit1.ndx"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]one" " no"
+.BI "-[no]one" "no "
Only write the fitted structure to file
-.BI "-[no]mw" " yes"
+.BI "-[no]mw" "yes "
Mass-weighted fitting and RMSD
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Try to make molecules whole again
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Do least squares superposition of the target structure to the reference
-.BI "-[no]name" " no"
+.BI "-[no]name" "no "
Only compare matching atom names
-.BI "-[no]bfac" " no"
+.BI "-[no]label" "no "
+ Added chain labels A for first and B for second structure
+
+.BI "-[no]bfac" "no "
Output B-factors from atomic MSD values
-.TH g_covar 1 "Mon 29 Aug 2005"
+.TH g_covar 1 "Mon 22 Sep 2008"
.SH NAME
g_covar
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_covar\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-v" " eigenvec.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-av" " average.pdb"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-l" " covar.log"
.B Output
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Fit to a reference structure
-.BI "-[no]ref" " no"
+.BI "-[no]ref" "no "
Use the deviation from the conformation in the structure file instead of from the average
-.BI "-[no]mwa" " no"
+.BI "-[no]mwa" "no "
Mass-weighted covariance analysis
.BI "-last" " int" " -1"
Last eigenvector to write away (-1 is till the last)
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Apply corrections for periodic boundary conditions
--- /dev/null
+.TH g_current 1 "Mon 22 Sep 2008"
+.SH NAME
+g_current
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_current\fP
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-f" " traj.xtc "
+.BI "-o" " current.xvg "
+.BI "-caf" " caf.xvg "
+.BI "-dsp" " dsp.xvg "
+.BI "-md" " md.xvg "
+.BI "-mj" " mj.xvg "
+.BI "-mc" " mc.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-sh" " int "
+.BI "-[no]nojump" ""
+.BI "-eps" " real "
+.BI "-bfit" " real "
+.BI "-efit" " real "
+.BI "-bvit" " real "
+.BI "-evit" " real "
+.BI "-tr" " real "
+.BI "-temp" " real "
+.SH DESCRIPTION
+This is a tool for calculating the current autocorrelation function, the correlation
+of the rotational and translational dipole moment of the system, and the resulting static
+dielectric constant. To obtain a reasonable result the index group has to be neutral.
+Furthermore the routine is capable of extracting the static conductivity from the current
+autocorrelation function, if velocities are given. Additionally an Einstein-Helfand fit also
+allows to get the static conductivity.
+
+
+The flag
+.B -caf
+is for the output of the current autocorrelation function and
+.B -mc
+writes the
+correlation of the rotational and translational part of the dipole moment in the corresponding
+file. However this option is only available for trajectories containing velocities.Options
+.B -sh
+and
+.B -tr
+are responsible for the averaging and integration of the
+autocorrelation functions. Since averaging proceeds by shifting the starting point
+through the trajectory, the shift can be modified with
+.B -sh
+to enable the choice of uncorrelated
+starting points. Towards the end, statistical inaccuracy grows and integrating the
+correlation function only yields reliable values until a certain point, depending on
+the number of frames. The option
+.B -tr
+controls the region of the integral taken into account
+for calculating the static dielectric constant.
+
+
+
+Option
+.B -temp
+sets the temperature required for the computation of the static dielectric constant.
+
+
+Option
+.B -eps
+controls the dielectric constant of the surrounding medium for simulations using
+a Reaction Field or dipole corrections of the Ewald summation (eps=0 corresponds to
+tin-foil boundary conditions).
+
+
+
+
+.B -[no]nojump
+unfolds the coordinates to allow free diffusion. This is required to get a continuous
+translational dipole moment, required for the Einstein-Helfand fit. The resuls from the fit allow to
+determine the dielectric constant for system of charged molecules. However it is also possible to extract
+the dielectric constant from the fluctuations of the total dipole moment in folded coordinates. But this
+options has to be used with care, since only very short time spans fulfill the approximation, that the density
+of the molecules is approximately constant and the averages are already converged. To be on the safe side,
+the dielectric constant should be calculated with the help of the Einstein-Helfand method for
+the translational part of the dielectric constant.
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-o" " current.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-caf" " caf.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-dsp" " dsp.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-md" " md.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-mj" " mj.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-mc" " mc.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-sh" " int" " 1000"
+ Shift of the frames for averaging the correlation functions and the mean-square displacement.
+
+.BI "-[no]nojump" "yes "
+ Removes jumps of atoms across the box.
+
+.BI "-eps" " real" " 0 "
+ Dielectric constant of the surrounding medium. eps=0.0 corresponds to eps=infinity (thinfoil boundary conditions).
+
+.BI "-bfit" " real" " 100 "
+ Begin of the fit of the straight line to the MSD of the translational fraction of the dipole moment.
+
+.BI "-efit" " real" " 400 "
+ End of the fit of the straight line to the MSD of the translational fraction of the dipole moment.
+
+.BI "-bvit" " real" " 0.5 "
+ Begin of the fit of the current autocorrelation function to a*tb.
+
+.BI "-evit" " real" " 5 "
+ End of the fit of the current autocorrelation function to a*tb.
+
+.BI "-tr" " real" " 0.25 "
+ Fraction of the trajectory taken into account for the integral.
+
+.BI "-temp" " real" " 300 "
+ Temperature for calculating epsilon.
+
-.TH g_density 1 "Mon 29 Aug 2005"
+.TH g_density 1 "Mon 22 Sep 2008"
.SH NAME
g_density
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_density\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-d" " string "
.BI "-sl" " int "
-.BI "-[no]number" ""
-.BI "-[no]ed" ""
-.BI "-[no]count" ""
+.BI "-dens" " enum "
.BI "-ng" " int "
.BI "-[no]symm" ""
.BI "-[no]center" ""
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-ei" " electrons.dat"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
Take the normal on the membrane in direction X, Y or Z.
-.BI "-sl" " int" " 10"
+.BI "-sl" " int" " 50"
Divide the box in nr slices.
-.BI "-[no]number" " no"
- Calculate number density instead of mass density. Hydrogens are not counted!
+.BI "-dens" " enum" " mass"
+ Density:
+.B mass
+,
+.B number
+,
+.B charge
+or
+.B electron
-.BI "-[no]ed" " no"
- Calculate electron density instead of mass density
-.BI "-[no]count" " no"
- Only count atoms in slices, no densities. Hydrogens are not counted
-
-.BI "-ng" " int" " 0"
+.BI "-ng" " int" " 1"
Number of groups to compute densities of
-.BI "-[no]symm" " no"
+.BI "-[no]symm" "no "
Symmetrize the density along the axis, with respect to the center. Useful for bilayers.
-.BI "-[no]center" " no"
+.BI "-[no]center" "no "
Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0.
+.SH KNOWN PROBLEMS
\- When calculating electron densities, atomnames are used instead of types. This is bad.
-\- When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.
-
-.TH g_densmap 1 "Mon 29 Aug 2005"
+.TH g_densmap 1 "Mon 22 Sep 2008"
.SH NAME
g_densmap
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_densmap\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-bin" " real "
-.BI "-nx" " int "
-.BI "-nz" " int "
+.BI "-aver" " enum "
+.BI "-xmin" " real "
+.BI "-xmax" " real "
+.BI "-n1" " int "
+.BI "-n2" " int "
.BI "-amax" " real "
.BI "-rmax" " real "
.BI "-[no]mirror" ""
+.BI "-unit" " enum "
+.BI "-dmin" " real "
.BI "-dmax" " real "
.SH DESCRIPTION
g_densmap computes 2D number-density maps.
The default analysis is a 2-D number-density map for a selected
-group of atoms in the x-z plane. The grid spacing is set with the option
-
+group of atoms in the x-y plane.
+The averaging direction can be changed with the option
+.B -aver
+.
+When
+.B -xmin
+and/or
+.B -xmax
+are set only atoms that are
+within the limit(s) in the averaging direction are taken into account.
+The grid spacing is set with the option
.B -bin
-. When
-.B -nx
+.
+When
+.B -n1
or
-.B -nz
+.B -n2
is non-zero, the grid
-size is set by this option. Box size fluctuations are properly taken
-into account.
+size is set by this option.
+Box size fluctuations are properly taken into account.
+The normalization of the output is set with the
+.B -unit
+option.
+The default produces a true number density. Unit
+.B nm-2
+leaves out
+the normalization for the averaging or the angular direction.
+Option
+.B count
+produces the count for each grid cell.
When you do not want the scale in the output to go
from zero to the maximum density, you can set the maximum
with the option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-bin" " real" " 0.02"
- Grid size
+.BI "-bin" " real" " 0.02 "
+ Grid size (nm)
+
+.BI "-aver" " enum" " z"
+ The direction to average over:
+.B z
+,
+.B y
+or
+.B x
+
-.BI "-nx" " int" " 0"
- Number of grid cells in x direction
+.BI "-xmin" " real" " -1 "
+ Minimum coordinate for averaging
-.BI "-nz" " int" " 0"
- Number of grid cells in z direction
+.BI "-xmax" " real" " -1 "
+ Maximum coordinate for averaging
-.BI "-amax" " real" " 0"
+.BI "-n1" " int" " 0"
+ Number of grid cells in the first direction
+
+.BI "-n2" " int" " 0"
+ Number of grid cells in the second direction
+
+.BI "-amax" " real" " 0 "
Maximum axial distance from the center
-.BI "-rmax" " real" " 0"
+.BI "-rmax" " real" " 0 "
Maximum radial distance
-.BI "-[no]mirror" " no"
+.BI "-[no]mirror" "no "
Add the mirror image below the axial axis
-.BI "-dmax" " real" " 0"
- Maximum density (0 means calculate it)
+.BI "-unit" " enum" " nm-3"
+ Unit for the output:
+.B nm-3
+,
+.B nm-2
+or
+.B count
+
+
+.BI "-dmin" " real" " 0 "
+ Minimum density in output
+
+.BI "-dmax" " real" " 0 "
+ Maximum density in output (0 means calculate it)
-.TH g_dielectric 1 "Mon 29 Aug 2005"
+.TH g_dielectric 1 "Mon 22 Sep 2008"
.SH NAME
g_dielectric
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dielectric\fP
-.BI "-f" " Mtot.xvg "
+.BI "-f" " dipcorr.xvg "
.BI "-d" " deriv.xvg "
.BI "-o" " epsw.xvg "
.BI "-c" " cole.xvg "
For a pure exponential relaxation (Debye relaxation) the latter
plot should be one half of a circle
.SH FILES
-.BI "-f" " Mtot.xvg"
+.BI "-f" " dipcorr.xvg"
.B Input
xvgr/xmgr file
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fft" " no"
+.BI "-[no]fft" "no "
use fast fourier transform for correlation function
-.BI "-[no]x1" " yes"
+.BI "-[no]x1" "yes "
use first column as X axis rather than first data set
-.BI "-eint" " real" " 5"
+.BI "-eint" " real" " 5 "
Time were to end the integration of the data and start to use the fit
-.BI "-bfit" " real" " 5"
+.BI "-bfit" " real" " 5 "
Begin time of fit
-.BI "-efit" " real" " 500"
+.BI "-efit" " real" " 500 "
End time of fit
-.BI "-tail" " real" " 500"
+.BI "-tail" " real" " 500 "
Length of function including data and tail from fit
-.BI "-A" " real" " 0.5"
+.BI "-A" " real" " 0.5 "
Start value for fit parameter A
-.BI "-tau1" " real" " 10"
+.BI "-tau1" " real" " 10 "
Start value for fit parameter tau1
-.BI "-tau2" " real" " 1"
+.BI "-tau2" " real" " 1 "
Start value for fit parameter tau2
-.BI "-eps0" " real" " 80"
+.BI "-eps0" " real" " 80 "
Epsilon 0 of your liquid
-.BI "-epsRF" " real" " 78.5"
+.BI "-epsRF" " real" " 78.5 "
Epsilon of the reaction field used in your simulation. A value of 0 means infinity.
.BI "-fix" " int" " 0"
-.TH g_dih 1 "Mon 29 Aug 2005"
+.TH g_dih 1 "Mon 22 Sep 2008"
.SH NAME
g_dih
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dih\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " hello.out"
.B Output
Generic output file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]sa" " no"
+.BI "-[no]sa" "no "
Perform cluster analysis in dihedral space instead of analysing dihedral transitions.
.BI "-mult" " int" " -1"
-.TH g_dipoles 1 "Mon 29 Aug 2005"
+.TH g_dipoles 1 "Mon 22 Sep 2008"
.SH NAME
g_dipoles
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "-enx" " ener.edr "
.BI "-adip" " adip.xvg "
.BI "-dip3d" " dip3d.xvg "
.BI "-cos" " cosaver.xvg "
+.BI "-cmap" " cmap.xpm "
.BI "-q" " quadrupole.xvg "
.BI "-slab" " slab.xvg "
.BI "-[no]h" ""
.BI "-epsilonRF" " real "
.BI "-skip" " int "
.BI "-temp" " real "
-.BI "-[no]avercorr" ""
+.BI "-corr" " enum "
.BI "-[no]pairs" ""
+.BI "-ncos" " int "
.BI "-axis" " string "
.BI "-sl" " int "
.BI "-gkratom" " int "
+.BI "-gkratom2" " int "
+.BI "-rcmax" " real "
+.BI "-[no]phi" ""
+.BI "-nlevels" " int "
+.BI "-ndegrees" " int "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-P" " enum "
.SH DESCRIPTION
g_dipoles computes the total dipole plus fluctuations of a simulation
system. From this you can compute e.g. the dielectric constant for
-low dielectric media
+low dielectric media.
+For molecules with a net charge, the net charge is subtracted at
+center of mass of the molecule.
The file Mtot.xvg contains the total dipole moment of a frame, the
The mu_max is used as the highest value in the distribution graph.
-Furthermore the dipole autocorrelation function will be computed, when
-option -c is used. It can be averaged over all molecules,
-or (with option -avercorr) it can be computed as the autocorrelation
-of the total dipole moment of the simulation box.
+Furthermore the dipole autocorrelation function will be computed when
+option -corr is used. The output file name is given with the
+.B -c
-
-At the moment the dielectric constant is calculated only correct if
-a rectangular or cubic simulation box is used.
+option.
+The correlation functions can be averaged over all molecules
+(
+.B mol
+), plotted per molecule seperately (
+.B molsep
+)
+or it can be computed over the total dipole moment of the simulation box
+(
+.B total
+).
Option
EXAMPLES
-g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
--nofft
+g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft
This will calculate the autocorrelation function of the molecular
.SH FILES
.BI "-enx" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-cmap" " cmap.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.BI "-q" " quadrupole.xvg"
.B Output, Opt.
xvgr/xmgr file
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-mu" " real" " -1"
+.BI "-mu" " real" " -1 "
dipole of a single molecule (in Debye)
-.BI "-mumax" " real" " 5"
+.BI "-mumax" " real" " 5 "
max dipole in Debye (for histrogram)
-.BI "-epsilonRF" " real" " 0"
+.BI "-epsilonRF" " real" " 0 "
epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default)
.BI "-skip" " int" " 0"
Skip steps in the output (but not in the computations)
-.BI "-temp" " real" " 300"
- average temperature of the simulation (needed for dielectric constant calculation)
+.BI "-temp" " real" " 300 "
+ Average temperature of the simulation (needed for dielectric constant calculation)
+
+.BI "-corr" " enum" " none"
+ Correlation function to calculate:
+.B none
+,
+.B mol
+,
+.B molsep
+or
+.B total
-.BI "-[no]avercorr" " no"
- calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule
-.BI "-[no]pairs" " yes"
+.BI "-[no]pairs" "yes "
Calculate |cos theta| between all pairs of molecules. May be slow
+.BI "-ncos" " int" " 1"
+ Must be 1 or 2. Determines whether the cos is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag.
+
.BI "-axis" " string" " Z"
Take the normal on the computational box in direction X, Y or Z.
.BI "-gkratom" " int" " 0"
Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors
+.BI "-gkratom2" " int" " 0"
+ Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules
+
+.BI "-rcmax" " real" " 0 "
+ Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used.
+
+.BI "-[no]phi" "no "
+ Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the xpm file from the -cmap option. By default the cosine of the angle between the dipoles is plotted.
+
+.BI "-nlevels" " int" " 20"
+ Number of colors in the cmap output
+
+.BI "-ndegrees" " int" " 90"
+ Number of divisions on the y-axis in the camp output (for 180 degrees)
+
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_disre 1 "Mon 29 Aug 2005"
+.TH g_disre 1 "Mon 22 Sep 2008"
.SH NAME
g_disre
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_disre\fP
.BI "-s" " topol.tpr "
.BI "-n" " viol.ndx "
.BI "-q" " viol.pdb "
.BI "-c" " clust.ndx "
+.BI "-x" " matrix.xpm "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
.BI "-ntop" " int "
+.BI "-maxdr" " real "
+.BI "-nlevels" " int "
+.BI "-[no]third" ""
.SH DESCRIPTION
g_disre computes violations of distance restraints.
If necessary all protons can be added to a protein molecule
using the protonate program.
-The program allways
+The program always
computes the instantaneous violations rather than time-averaged,
because this analysis is done from a trajectory file afterwards
it does not make sense to use time averaging. However,
option is given, an index file will be read
containing the frames in your trajectory corresponding to the clusters
(defined in another manner) that you want to analyze. For these clusters
-the program will compute average violations using the thisd power
+the program will compute average violations using the third power
averaging algorithm and print them in the log file.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-ds" " drsum.xvg"
.B Output
.B Input, Opt.
Index file
+.BI "-x" " matrix.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-ntop" " int" " 0"
Number of large violations that are stored in the log file every step
+.BI "-maxdr" " real" " 0 "
+ Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data.
+
+.BI "-nlevels" " int" " 20"
+ Number of levels in the matrix output
+
+.BI "-[no]third" "yes "
+ Use inverse third power averaging or linear for matrix output
+
-.TH g_dist 1 "Mon 29 Aug 2005"
+.TH g_dist 1 "Mon 22 Sep 2008"
.SH NAME
g_dist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dist\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-o" " dist.xvg "
+.BI "-lt" " lifetime.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
closer than a certain distance to the center of mass of group 1.
+With options
+.B -lt
+and
+.B -dist
+the number of contacts
+of all atoms in group 2 that are closer than a certain distance
+to the center of mass of group 1 are plotted as a function of the time
+that the contact was continously present.
+
+
Other programs that calculate distances are
.B g_mindist
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-lt" " lifetime.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-dist" " real" " 0"
+.BI "-dist" " real" " 0 "
Print all atoms in group 2 closer than dist to the center of mass of group 1
-.TH g_dyndom 1 "Mon 29 Aug 2005"
+.TH g_dyndom 1 "Mon 22 Sep 2008"
.SH NAME
g_dyndom
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "-f" " dyndom.pdb "
.BI "-tail" " vector "
.SH DESCRIPTION
g_dyndom reads a pdb file output from DynDom
-http://md.chem.rug.nl/~steve/DynDom/dyndom.home.html
+http://www.cmp.uea.ac.uk/dyndom/
It reads the coordinates, and the coordinates of the rotation axis
furthermore it reads an index file containing the domains.
Furthermore it takes the first and last atom of the arrow file
.BI "-o" " rotated.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-n" " domains.ndx"
.B Input
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-firstangle" " real" " 0"
+.BI "-firstangle" " real" " 0 "
Angle of rotation about rotation vector
-.BI "-lastangle" " real" " 0"
+.BI "-lastangle" " real" " 0 "
Angle of rotation about rotation vector
.BI "-nframe" " int" " 11"
Number of steps on the pathway
-.BI "-maxangle" " real" " 0"
+.BI "-maxangle" " real" " 0 "
DymDom dtermined angle of rotation about rotation vector
-.BI "-trans" " real" " 0"
+.BI "-trans" " real" " 0 "
Translation (Aangstroem) along rotation vector (see DynDom info file)
.BI "-head" " vector" " 0 0 0"
-.TH g_enemat 1 "Mon 29 Aug 2005"
+.TH g_enemat 1 "Mon 22 Sep 2008"
.SH NAME
g_enemat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_enemat\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-groups" " groups.dat"
.B Input
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]sum" " no"
+.BI "-[no]sum" "no "
Sum the energy terms selected rather than display them all
.BI "-skip" " int" " 0"
Skip number of frames between data points
-.BI "-[no]mean" " yes"
+.BI "-[no]mean" "yes "
with -groups extracts matrix of mean energies in stead of matrix for each timestep
.BI "-nlevels" " int" " 20"
number of levels for matrix colors
-.BI "-max" " real" " 1e+20"
+.BI "-max" " real" " 1e+20 "
max value for energies
.BI "-min" " real" " -1e+20"
min value for energies
-.BI "-[no]coul" " yes"
+.BI "-[no]coul" "yes "
extract Coulomb SR energies
-.BI "-[no]coulr" " no"
+.BI "-[no]coulr" "no "
extract Coulomb LR energies
-.BI "-[no]coul14" " no"
+.BI "-[no]coul14" "no "
extract Coulomb 1-4 energies
-.BI "-[no]lj" " yes"
+.BI "-[no]lj" "yes "
extract Lennard-Jones SR energies
-.BI "-[no]lj" " no"
+.BI "-[no]lj" "no "
extract Lennard-Jones LR energies
-.BI "-[no]lj14" " no"
+.BI "-[no]lj14" "no "
extract Lennard-Jones 1-4 energies
-.BI "-[no]bhamsr" " no"
+.BI "-[no]bhamsr" "no "
extract Buckingham SR energies
-.BI "-[no]bhamlr" " no"
+.BI "-[no]bhamlr" "no "
extract Buckingham LR energies
-.BI "-[no]free" " yes"
+.BI "-[no]free" "yes "
calculate free energy
-.BI "-temp" " real" " 300"
+.BI "-temp" " real" " 300 "
reference temperature for free energy calculation
-.TH g_energy 1 "Mon 29 Aug 2005"
+.TH g_energy 1 "Mon 22 Sep 2008"
.SH NAME
g_energy
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_energy\fP
.BI "-f" " ener.edr "
.BI "-[no]sum" ""
.BI "-[no]dp" ""
.BI "-[no]mutot" ""
+.BI "-[no]uni" ""
.BI "-skip" " int "
.BI "-[no]aver" ""
.BI "-nmol" " int "
Average and RMSD are calculated with full precision from the
simulation (see printed manual). Drift is calculated by performing
a LSQ fit of the data to a straight line. Total drift is drift
-multiplied by total time.
+multiplied by total time. The term fluctuation gives the RMSD around
+the LSQ fit.
When the
.SH FILES
.BI "-f" " ener.edr"
.B Input
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-f2" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " energy.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]fee" " no"
+.BI "-[no]fee" "no "
Do a free energy estimate
-.BI "-fetemp" " real" " 300"
+.BI "-fetemp" " real" " 300 "
Reference temperature for free energy calculation
-.BI "-zero" " real" " 0"
+.BI "-zero" " real" " 0 "
Subtract a zero-point energy
-.BI "-[no]sum" " no"
+.BI "-[no]sum" "no "
Sum the energy terms selected rather than display them all
-.BI "-[no]dp" " no"
+.BI "-[no]dp" "no "
Print energies in high precision
-.BI "-[no]mutot" " no"
+.BI "-[no]mutot" "no "
Compute the total dipole moment from the components
+.BI "-[no]uni" "yes "
+ Skip non-uniformly spaced frames
+
.BI "-skip" " int" " 0"
Skip number of frames between data points
-.BI "-[no]aver" " no"
+.BI "-[no]aver" "no "
Print also the X1,t and sigma1,t, only if only 1 energy is requested
.BI "-nmol" " int" " 1"
.BI "-ndf" " int" " 3"
Number of degrees of freedom per molecule. Necessary for calculating the heat capacity
-.BI "-[no]fluc" " no"
+.BI "-[no]fluc" "no "
Calculate autocorrelation of energy fluctuations rather than energy itself
-.BI "-[no]orinst" " no"
+.BI "-[no]orinst" "no "
Analyse instantaneous orientation data
-.BI "-[no]ovec" " no"
+.BI "-[no]ovec" "no "
Also plot the eigenvectors with -oten
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_filter 1 "Mon 29 Aug 2005"
+.TH g_filter 1 "Mon 22 Sep 2008"
.SH NAME
g_filter
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_filter\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-ol" " lowpass.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-oh" " highpass.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
.BI "-nf" " int" " 10"
Sets the filter length as well as the output interval for low-pass filtering
-.BI "-[no]all" " no"
+.BI "-[no]all" "no "
Write all low-pass filtered frames
-.BI "-[no]nojump" " yes"
+.BI "-[no]nojump" "yes "
Remove jumps of atoms across the box
-.BI "-[no]fit" " no"
+.BI "-[no]fit" "no "
Fit all frames to a reference structure
-.TH g_gyrate 1 "Mon 29 Aug 2005"
+.TH g_gyrate 1 "Mon 22 Sep 2008"
.SH NAME
g_gyrate
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "-f" " traj.xtc "
.BI "-[no]q" ""
.BI "-[no]p" ""
.BI "-[no]moi" ""
+.BI "-nz" " int "
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.BI "-P" " enum "
g_gyrate computes the radius of gyration of a group of atoms
and the radii of gyration about the x, y and z axes,
as a function of time. The atoms are explicitly mass weighted.
+
+
With the
.B -nmol
option the radius of gyration will be calculated
for multiple molecules by splitting the analysis group in equally
sized parts.
+
+
+With the option
+.B -nz
+2D radii of gyration in the x-y plane
+of slices along the z-axis are calculated.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-nmol" " int" " 1"
The number of molecules to analyze
-.BI "-[no]q" " no"
+.BI "-[no]q" "no "
Use absolute value of the charge of an atom as weighting factor instead of mass
-.BI "-[no]p" " no"
+.BI "-[no]p" "no "
Calculate the radii of gyration about the principal axes.
-.BI "-[no]moi" " no"
- Calculate the moments of inertia (defined by the principal axes).
+.BI "-[no]moi" "no "
+ Calculate the moments of inertia (defined by the principal axes).
+
+.BI "-nz" " int" " 0"
+ Calculate the 2D radii of gyration of slices along the z-axis
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_h2order 1 "Mon 29 Aug 2005"
+.TH g_h2order 1 "Mon 22 Sep 2008"
.SH NAME
g_h2order
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_h2order\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " order.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
.BI "-sl" " int" " 0"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
+.SH KNOWN PROBLEMS
\- The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different.
-.TH g_hbond 1 "Mon 29 Aug 2005"
+.TH g_hbond 1 "Mon 22 Sep 2008"
.SH NAME
g_hbond
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_hbond\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
-.BI "-g" " hbond.log "
-.BI "-sel" " select.ndx "
.BI "-num" " hbnum.xvg "
+.BI "-g" " hbond.log "
.BI "-ac" " hbac.xvg "
.BI "-dist" " hbdist.xvg "
.BI "-ang" " hbang.xvg "
.BI "-don" " donor.xvg "
.BI "-dan" " danum.xvg "
.BI "-life" " hblife.xvg "
+.BI "-nhbdist" " nhbdist.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-a" " real "
.BI "-r" " real "
.BI "-[no]da" ""
+.BI "-r2" " real "
.BI "-abin" " real "
.BI "-rbin" " real "
.BI "-[no]nitacc" ""
.BI "-shell" " real "
.BI "-fitstart" " real "
.BI "-temp" " real "
+.BI "-smooth" " real "
.BI "-dump" " int "
.BI "-max_hb" " real "
.BI "-[no]merge" ""
.BI "-endfit" " real "
.SH DESCRIPTION
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
-determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
+determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
(zero is extended) and the distance Hydrogen - Acceptor.
OH and NH groups are regarded as donors, O is an acceptor always,
N is an acceptor by default, but this can be switched using
bonds between atoms within the shell distance from the one atom are
considered.
-It is also possible to analyse specific hydrogen bonds with
-
-.B -sel
-. This index file must contain a group of atom triplets
-Donor Hydrogen Acceptor, in the following way:
-
-
.B
[ selected ]
.
+.B -nhbdist
+: compute the number of HBonds per hydrogen in order to
+compare results to Raman Spectroscopy.
+
+
Note: options
.B -ac
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
-.BI "-g" " hbond.log"
-.B Output, Opt.
- Log file
-
-.BI "-sel" " select.ndx"
-.B Input, Opt.
- Index file
-
.BI "-num" " hbnum.xvg"
.B Output
xvgr/xmgr file
+.BI "-g" " hbond.log"
+.B Output, Opt.
+ Log file
+
.BI "-ac" " hbac.xvg"
.B Output, Opt.
xvgr/xmgr file
.B Output, Opt.
xvgr/xmgr file
+.BI "-nhbdist" " nhbdist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]ins" " no"
+.BI "-[no]ins" "no "
Analyze solvent insertion
-.BI "-a" " real" " 30"
- Cutoff angle (degrees, Donor - Hydrogen - Acceptor)
+.BI "-a" " real" " 30 "
+ Cutoff angle (degrees, Acceptor - Donor - Hydrogen)
-.BI "-r" " real" " 0.35"
+.BI "-r" " real" " 0.35 "
Cutoff radius (nm, X - Acceptor, see next option)
-.BI "-[no]da" " yes"
+.BI "-[no]da" "yes "
Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE)
-.BI "-abin" " real" " 1"
+.BI "-r2" " real" " 0 "
+ Second cutoff radius. Mainly useful with -contact and -ac
+
+.BI "-abin" " real" " 1 "
Binwidth angle distribution (degrees)
-.BI "-rbin" " real" " 0.005"
+.BI "-rbin" " real" " 0.005 "
Binwidth distance distribution (nm)
-.BI "-[no]nitacc" " yes"
+.BI "-[no]nitacc" "yes "
Regard nitrogen atoms as acceptors
-.BI "-[no]contact" " no"
+.BI "-[no]contact" "no "
Do not look for hydrogen bonds, but merely for contacts within the cut-off distance
-.BI "-shell" " real" " -1"
+.BI "-shell" " real" " -1 "
when 0, only calculate hydrogen bonds within nm shell around one particle
-.BI "-fitstart" " real" " 1"
- Time from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
+.BI "-fitstart" " real" " 1 "
+ Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation
.BI "-temp" " real" " 298.15"
Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming
+.BI "-smooth" " real" " -1 "
+ If = 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau)
+
.BI "-dump" " int" " 0"
Dump the first N hydrogen bond ACFs in a single xvg file for debugging
-.BI "-max_hb" " real" " 0"
+.BI "-max_hb" " real" " 0 "
Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly
-.BI "-[no]merge" " yes"
+.BI "-[no]merge" "yes "
H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF.
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
+.SH KNOWN PROBLEMS
+\- The option
+.B -sel
+that used to work on selected hbonds is out of order, and therefore not available for the time being.
+
-.TH g_helix 1 "Mon 29 Aug 2005"
+.TH g_helix 1 "Mon 22 Sep 2008"
.SH NAME
g_helix
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_helix\fP
.BI "-s" " topol.tpr "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-to" " gtraj.g87"
.B Output, Opt.
.BI "-cz" " zconf.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-co" " waver.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
.BI "-r0" " int" " 1"
The first residue number in the sequence
-.BI "-[no]q" " no"
+.BI "-[no]q" "no "
Check at every step which part of the sequence is helical
-.BI "-[no]F" " yes"
+.BI "-[no]F" "yes "
Toggle fit to a perfect helix
-.BI "-[no]db" " no"
+.BI "-[no]db" "no "
Print debug info
.BI "-prop" " enum" " RAD"
.B CD222
-.BI "-[no]ev" " no"
+.BI "-[no]ev" "no "
Write a new 'trajectory' file for ED
.BI "-ahxstart" " int" " 0"
--- /dev/null
+.TH g_helixorient 1 "Mon 22 Sep 2008"
+.SH NAME
+g_helixorient
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_helixorient\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-oaxis" " helixaxis.dat "
+.BI "-ocenter" " center.dat "
+.BI "-orise" " rise.xvg "
+.BI "-oradius" " radius.xvg "
+.BI "-otwist" " twist.xvg "
+.BI "-obending" " bending.xvg "
+.BI "-otilt" " tilt.xvg "
+.BI "-orot" " rotation.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]xvgr" ""
+.BI "-[no]sidechain" ""
+.BI "-[no]incremental" ""
+.SH DESCRIPTION
+g_helixorient calculates coordinates and direction of the average
+axis inside an alpha helix, and the direction/vectors of both the
+alpha carbon and (optionally) a sidechain atom relative to the axis.
+
+
+As input, you need to specify an index group with alpha carbon atoms
+corresponding to an alpha helix of continuous residues. Sidechain
+directions require a second index group of the same size, containing
+the heavy atom in each residue that should represent the sidechain.
+
+Note that this program does not do any fitting of structures.
+
+
+We need four Calpha coordinates to define the local direction of the helix
+axis.
+
+The tilt/rotation is calculated from Euler rotations, where we define
+the helix axis as the local X axis, the residues/CA-vector as Y, and the
+Z axis from their cross product. We use the Euler Y-Z-X rotation, meaning
+we first tilt the helix axis (1) around and (2) orthogonal to the residues
+vector, and finally apply the (3) rotation around it. For debugging or other
+purposes, we also write out the actual Euler rotation angles as theta1-3.xvg
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Run input file: tpr tpb tpa
+
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-oaxis" " helixaxis.dat"
+.B Output
+ Generic data file
+
+.BI "-ocenter" " center.dat"
+.B Output
+ Generic data file
+
+.BI "-orise" " rise.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-oradius" " radius.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-otwist" " twist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-obending" " bending.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-otilt" " tilt.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-orot" " rotation.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-[no]sidechain" "no "
+ Calculate sidechain directions relative to helix axis too.
+
+.BI "-[no]incremental" "no "
+ Calculate incremental rather than total rotation/tilt.
+
-.TH g_lie 1 "Mon 29 Aug 2005"
+.TH g_lie 1 "Mon 22 Sep 2008"
.SH NAME
g_lie
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_lie\fP
.BI "-f" " ener.edr "
.SH FILES
.BI "-f" " ener.edr"
.B Input
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-o" " lie.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-Elj" " real" " 0"
+.BI "-Elj" " real" " 0 "
Lennard-Jones interaction between ligand and solvent
-.BI "-Eqq" " real" " 0"
+.BI "-Eqq" " real" " 0 "
Coulomb interaction between ligand and solvent
-.BI "-Clj" " real" " 0.181"
+.BI "-Clj" " real" " 0.181 "
Factor in the LIE equation for Lennard-Jones component of energy
-.BI "-Cqq" " real" " 0.5"
+.BI "-Cqq" " real" " 0.5 "
Factor in the LIE equation for Coulomb component of energy
.BI "-ligand" " string" " none"
-.TH g_mdmat 1 "Mon 29 Aug 2005"
+.TH g_mdmat 1 "Mon 22 Sep 2008"
.SH NAME
g_mdmat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-t" " real" " 1.5"
+.BI "-t" " real" " 1.5 "
trunc distance
.BI "-nlevels" " int" " 40"
-.TH g_mindist 1 "Mon 29 Aug 2005"
+.TH g_mindist 1 "Mon 22 Sep 2008"
.SH NAME
g_mindist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_mindist\fP
.BI "-f" " traj.xtc "
.BI "-[no]pi" ""
.BI "-[no]split" ""
.BI "-ng" " int "
+.BI "-[no]pbc" ""
.SH DESCRIPTION
g_mindist computes the distance between one group and a number of
other groups. Both the minimum distance
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-ox" " mindist.xtc"
.B Output, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-or" " mindistres.xvg"
.B Output, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]matrix" " no"
+.BI "-[no]matrix" "no "
Calculate half a matrix of group-group distances
-.BI "-[no]max" " no"
+.BI "-[no]max" "no "
Calculate *maximum* distance instead of minimum
-.BI "-d" " real" " 0.6"
+.BI "-d" " real" " 0.6 "
Distance for contacts
-.BI "-[no]pi" " no"
+.BI "-[no]pi" "no "
Calculate minimum distance with periodic images
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split graph where time is zero
.BI "-ng" " int" " 1"
Number of secondary groups to compute distance to a central group
+.BI "-[no]pbc" "yes "
+ Take periodic boundary conditions into account
+
-.TH g_morph 1 "Mon 29 Aug 2005"
+.TH g_morph 1 "Mon 22 Sep 2008"
.SH NAME
g_morph
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_morph\fP
.BI "-f1" " conf1.gro "
.SH FILES
.BI "-f1" " conf1.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-f2" " conf2.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " interm.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-or" " rms-interm.xvg"
.B Output, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-ninterm" " int" " 11"
Number of intermediates
-.BI "-first" " real" " 0"
+.BI "-first" " real" " 0 "
Corresponds to first generated structure (0 is input x0, see above)
-.BI "-last" " real" " 1"
+.BI "-last" " real" " 1 "
Corresponds to last generated structure (1 is input x1, see above)
-.BI "-[no]fit" " yes"
+.BI "-[no]fit" "yes "
Do a least squares fit of the second to the first structure before interpolating
-.TH g_msd 1 "Mon 29 Aug 2005"
+.TH g_msd 1 "Mon 22 Sep 2008"
.SH NAME
g_msd
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_msd\fP
.BI "-f" " traj.xtc "
.BI "-n" " index.ndx "
.BI "-o" " msd.xvg "
.BI "-mol" " diff_mol.xvg "
+.BI "-pdb" " diff_mol.pdb "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]xvgr" ""
.BI "-type" " enum "
.BI "-lateral" " enum "
+.BI "-[no]ten" ""
.BI "-ngroup" " int "
.BI "-[no]mw" ""
+.BI "-[no]rmcomm" ""
+.BI "-tpdb" " time "
.BI "-trestart" " time "
.BI "-beginfit" " time "
.BI "-endfit" " time "
of the fit interval.
+There are three, mutually exclusive, options to determine different
+types of mean square displacement:
+.B -type
+,
+.B -lateral
+
+and
+.B -ten
+. Option
+.B -ten
+writes the full MSD tensor for
+each group, the order in the output is: trace xx yy zz yx zx zy.
+
+
Option
.B -mol
plots the MSD for molecules, this implies
+With option
+.B -rmcomm
+center of mass motion can be removed.
+For trajectories produced with GROMACS this is usually not necessary
+as mdrun usually already removes the center of mass motion.
+When you use this option be sure that the whole system is stored
+in the trajectory file.
+
+
.B -mw
, i.e. for each inidividual molecule an diffusion constant
-is computed. When using an index file, it should contain molecule
-numbers instead of atom numbers.
+is computed for its center of mass. The chosen index group will
+be split into molecules.
+The diffusion coefficient is determined by linear regression of the MSD,
+where, unlike for the normal output of D, the times are weighted
+according to the number of restart point, i.e. short times have
+a higher weight. Also when
+.B -beginfit
+=-1,fitting starts at 0
+and when
+.B -endfit
+=-1, fitting goes to the end.
Using this option one also gets an accurate error estimate
-based on the statistics between individual molecules. Since one usually
-is interested in self-diffusion at infinite dilution this is probably
-the most useful number.
+based on the statistics between individual molecules.
+Note that this diffusion coefficient and error estimate are only
+accurate when the MSD is completely linear between
+
+.B -beginfit
+and
+.B -endfit
+.
+Option
+.B -pdb
+writes a pdb file with the coordinates of the frame
+at time
+.B -tpdb
+with in the B-factor field the square root of
+the diffusion coefficient of the molecule.
+This option implies option
+.B -mol
+.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-pdb" " diff_mol.pdb"
+.B Output, Opt.
+ Protein data bank file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-type" " enum" " no"
.B z
+.BI "-[no]ten" "no "
+ Calculate the full tensor
+
.BI "-ngroup" " int" " 1"
Number of groups to calculate MSD for
-.BI "-[no]mw" " yes"
+.BI "-[no]mw" "yes "
Mass weighted MSD
-.BI "-trestart" " time" " 10"
+.BI "-[no]rmcomm" "no "
+ Remove center of mass motion
+
+.BI "-tpdb" " time" " 0 "
+ The frame to use for option -pdb (ps)
+
+.BI "-trestart" " time" " 10 "
Time between restarting points in trajectory (ps)
-.BI "-beginfit" " time" " -1"
+.BI "-beginfit" " time" " -1 "
Start time for fitting the MSD (ps), -1 is 10%
-.BI "-endfit" " time" " -1"
+.BI "-endfit" " time" " -1 "
End time for fitting the MSD (ps), -1 is 90%
-.TH g_nmeig 1 "Mon 29 Aug 2005"
+.TH g_nmeig 1 "Mon 22 Sep 2008"
.SH NAME
g_nmeig
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "-f" " hessian.mtx "
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-of" " eigenfreq.xvg"
.B Output
.BI "-v" " eigenvec.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]m" " yes"
+.BI "-[no]m" "yes "
Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis
.BI "-first" " int" " 1"
-.TH g_nmens 1 "Mon 29 Aug 2005"
+.TH g_nmens 1 "Mon 22 Sep 2008"
.SH NAME
g_nmens
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmens\fP
.BI "-v" " eigenvec.trr "
.SH FILES
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " eigenval.xvg"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " ensemble.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-temp" " real" " 300"
+.BI "-temp" " real" " 300 "
Temperature in Kelvin
.BI "-seed" " int" " -1"
-.TH g_nmtraj 1 "Tue 6 Sep 2005"
+.TH g_nmtraj 1 "Mon 22 Sep 2008"
.SH NAME
g_nmtraj
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "-s" " topol.tpr "
.BI "-o" " nmtraj.xtc "
.BI "-[no]h" ""
.BI "-nice" " int "
-.BI "-eignr" " int "
+.BI "-eignr" " string "
+.BI "-phases" " string "
.BI "-temp" " real "
.BI "-amplitude" " real "
.BI "-nframes" " int "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-v" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-o" " nmtraj.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-eignr" " int" " 7"
- Eigenvector to use (first is 1)
+.BI "-eignr" " string" " 7"
+ String of eigenvectors to use (first is 1)
-.BI "-temp" " real" " 300"
+.BI "-phases" " string" " 0.0"
+ String of phases (default is 0.0)
+
+.BI "-temp" " real" " 300 "
Temperature in Kelvin
-.BI "-amplitude" " real" " 0.25"
+.BI "-amplitude" " real" " 0.25 "
Amplitude for modes with eigenvalue=0
.BI "-nframes" " int" " 30"
-.TH g_order 1 "Mon 29 Aug 2005"
+.TH g_order 1 "Mon 22 Sep 2008"
.SH NAME
g_order
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_order\fP
.BI "-f" " traj.xtc "
.BI "-o" " order.xvg "
.BI "-od" " deuter.xvg "
.BI "-os" " sliced.xvg "
+.BI "-Sg" " sg-ang.xvg "
+.BI "-Sk" " sk-dist.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
order parameter per slice is calculated as well. If -szonly is not
selected, all diagonal elements and the deuterium order parameter is
given.
+
+The tetrahedrality order parameters can be determined
+around an atom. Both angle an distance order parameters are calculated. See
+P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
+for more details.
+
+
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " order.xvg"
.B Output
.B Output
xvgr/xmgr file
+.BI "-Sg" " sg-ang.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-Sk" " sk-dist.xvg"
+.B Output
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " enum" " z"
.BI "-sl" " int" " 1"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
-.BI "-[no]szonly" " no"
+.BI "-[no]szonly" "no "
Only give Sz element of order tensor. (axis can be specified with -d)
-.BI "-[no]unsat" " no"
+.BI "-[no]unsat" "no "
Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
--- /dev/null
+.TH g_polystat 1 "Mon 22 Sep 2008"
+.SH NAME
+g_polystat
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_polystat\fP
+.BI "-s" " topol.tpr "
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-o" " polystat.xvg "
+.BI "-v" " polyvec.xvg "
+.BI "-p" " persist.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-[no]mw" ""
+.BI "-[no]pc" ""
+.SH DESCRIPTION
+g_polystat plots static properties of polymers as a function of time
+and prints the average.
+
+
+By default it determines the average end-to-end distance and radii
+of gyration of polymers. It asks for an index group and split this
+into molecules. The end-to-end distance is then determined using
+the first and the last atom in the index group for each molecules.
+For the radius of gyration the total and the three principal components
+for the average gyration tensor are written.
+With option
+.B -v
+the eigenvectors are written.
+With option
+.B -pc
+also the average eigenvalues of the individual
+gyration tensors are written.
+
+
+With option
+.B -p
+the presistence length is determined.
+The chosen index group should consist of atoms that are
+consecutively bonded in the polymer mainchains.
+The presistence length is then determined from the cosine of
+the angles between bonds with an index difference that is even,
+the odd pairs are not used, because straight polymer backbones
+are usually all trans and therefore only every second bond aligns.
+The persistence length is defined as number of bonds where
+the average cos reaches a value of 1/e. This point is determined
+by a linear interpolation of log(cos).
+.SH FILES
+.BI "-s" " topol.tpr"
+.B Input
+ Run input file: tpr tpb tpa
+
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " polystat.xvg"
+.B Output
+ xvgr/xmgr file
+
+.BI "-v" " polyvec.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-p" " persist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+or
+.B s
+
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-[no]mw" "yes "
+ Use the mass weighting for radii of gyration
+
+.BI "-[no]pc" "no "
+ Plot average eigenvalues
+
-.TH g_potential 1 "Mon 29 Aug 2005"
+.TH g_potential 1 "Mon 22 Sep 2008"
.SH NAME
g_potential
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_potential\fP
.BI "-f" " traj.xtc "
.BI "-tz" " real "
.BI "-[no]spherical" ""
.BI "-ng" " int "
+.BI "-[no]correct" ""
.SH DESCRIPTION
Compute the electrostatical potential across the box. The potential iscalculated by first summing the charges per slice and then integratingtwice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side ofthe box. It's also possible to calculate the potential in sphericalcoordinates as function of r by calculating a charge distribution inspherical slices and twice integrating them. epsilon_r is taken as 1,2 is more appropriate in many cases
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " potential.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-d" " string" " Z"
.BI "-ce" " int" " 0"
Discard last nr slices of box for integration
-.BI "-tz" " real" " 0"
+.BI "-tz" " real" " 0 "
Translate all coordinates distance in the direction of the box
-.BI "-[no]spherical" " no"
+.BI "-[no]spherical" "no "
Calculate spherical thingie
.BI "-ng" " int" " 1"
Number of groups to consider
+.BI "-[no]correct" "no "
+ Assume net zero charge of groups to improve accuracy
+
+.SH KNOWN PROBLEMS
\- Discarding slices for integration should not be necessary.
--- /dev/null
+.TH g_principal 1 "Mon 22 Sep 2008"
+.SH NAME
+g_principal
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_principal\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-a1" " axis1.dat "
+.BI "-a2" " axis2.dat "
+.BI "-a3" " axis3.dat "
+.BI "-om" " moi.dat "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.SH DESCRIPTION
+g_principal calculates the three principal axes of inertion for a group
+of atoms.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-a1" " axis1.dat"
+.B Output
+ Generic data file
+
+.BI "-a2" " axis2.dat"
+.B Output
+ Generic data file
+
+.BI "-a3" " axis3.dat"
+.B Output
+ Generic data file
+
+.BI "-om" " moi.dat"
+.B Output
+ Generic data file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+or
+.B s
+
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
-.TH g_rama 1 "Mon 29 Aug 2005"
+.TH g_rama 1 "Mon 22 Sep 2008"
.SH NAME
g_rama
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rama\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " rama.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.TH g_rdf 1 "Mon 29 Aug 2005"
+.TH g_rdf 1 "Mon 22 Sep 2008"
.SH NAME
g_rdf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rdf\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-bin" " real "
.BI "-[no]com" ""
+.BI "-rdf" " enum "
.BI "-[no]pbc" ""
+.BI "-[no]norm" ""
.BI "-[no]xy" ""
.BI "-cut" " real "
.BI "-ng" " int "
.
+The option
+.B -rdf
+sets the type of rdf to be computed.
+Default is for atoms or particles, but one can also select center
+of mass or geometry of molecules or residues. In all cases only
+the atoms in the index groups are taken into account.
+For molecules and/or the center of mass option a run input file
+is required.
+Other weighting than COM or COG can currently only be achieved
+by providing a run input file with different masses.
+Option
+.B -com
+also works in conjunction with
+.B -rdf
+.
+
If a run input file is supplied (
.B -s
-), exclusions defined
+) and
+.B -rdf
+is set
+to
+.B atom
+, exclusions defined
in that file are taken into account when calculating the rdf.
The option
.B -cut
Option
.B -cn
-produces the cumulative number rdf.
+produces the cumulative number rdf,
+i.e. the average number of particles within a distance r.
+
To bridge the gap between theory and experiment structure factors can
be computed (option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-bin" " real" " 0.002"
+.BI "-bin" " real" " 0.002 "
Binwidth (nm)
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
RDF with respect to the center of mass of first group
-.BI "-[no]pbc" " yes"
- Use periodic boundary conditions for computing distances
+.BI "-rdf" " enum" " atom"
+ RDF type:
+.B atom
+,
+.B mol_com
+,
+.B mol_cog
+,
+.B res_com
+or
+.B res_cog
+
+
+.BI "-[no]pbc" "yes "
+ Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the larges box edge.
+
+.BI "-[no]norm" "yes "
+ Normalize for volume and density
-.BI "-[no]xy" " no"
+.BI "-[no]xy" "no "
Use only the x and y components of the distance
-.BI "-cut" " real" " 0"
+.BI "-cut" " real" " 0 "
Shortest distance (nm) to be considered
.BI "-ng" " int" " 1"
Number of secondary groups to compute RDFs around a central group
-.BI "-fade" " real" " 0"
+.BI "-fade" " real" " 0 "
From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)2 to make it go to 1 smoothly. If fade is 0.0 nothing is done.
.BI "-nlevel" " int" " 20"
Number of different colors in the diffraction image
-.BI "-startq" " real" " 0"
+.BI "-startq" " real" " 0 "
Starting q (1/nm)
-.BI "-endq" " real" " 60"
+.BI "-endq" " real" " 60 "
Ending q (1/nm)
-.BI "-energy" " real" " 12"
+.BI "-energy" " real" " 12 "
Energy of the incoming X-ray (keV)
-.TH g_rms 1 "Mon 29 Aug 2005"
+.TH g_rms 1 "Mon 22 Sep 2008"
.SH NAME
g_rms
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rms\fP
.BI "-s" " topol.tpr "
.BI "-min" " real "
.BI "-bmax" " real "
.BI "-bmin" " real "
+.BI "-[no]mw" ""
.BI "-nlevels" " int "
.BI "-ng" " int "
.SH DESCRIPTION
translation), translation only, or no fitting at all.
+Option
+.B -mw
+controls whether mass weighting is done or not.
+If you select the option (default) and
+supply a valid tpr file masses will be taken from there,
+otherwise the masses will be deduced from the atommass.dat file in
+the GROMACS library directory. This is fine for proteins but not
+necessarily for other molecules. A default mass of 12.011 amu (Carbon)
+is assigned to unknown atoms. You can check whether this happend by
+turning on the
+.B -debug
+flag and inspecting the log file.
+
+
With
.B -f2
, the 'other structures' are taken from a second
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-f2" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-what" " enum" " rmsd"
.B rhosc
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
PBC check
.BI "-fit" " enum" " rot+trans"
.BI "-prev" " int" " 0"
Compare with previous frame
-.BI "-[no]split" " no"
+.BI "-[no]split" "no "
Split graph where time is zero
.BI "-skip" " int" " 1"
.BI "-skip2" " int" " 1"
Only write every nr-th frame to matrix
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in comparison matrix
-.BI "-min" " real" " -1"
+.BI "-min" " real" " -1 "
Minimum level in comparison matrix
-.BI "-bmax" " real" " -1"
+.BI "-bmax" " real" " -1 "
Maximum level in bond angle matrix
-.BI "-bmin" " real" " -1"
+.BI "-bmin" " real" " -1 "
Minimum level in bond angle matrix
+.BI "-[no]mw" "yes "
+ Use mass weighting for superposition
+
.BI "-nlevels" " int" " 80"
Number of levels in the matrices
-.TH g_rmsdist 1 "Mon 29 Aug 2005"
+.TH g_rmsdist 1 "Mon 22 Sep 2008"
.SH NAME
g_rmsdist
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-nlevels" " int" " 40"
Discretize rms in levels
-.BI "-max" " real" " -1"
+.BI "-max" " real" " -1 "
Maximum level in matrices
-.BI "-[no]sumh" " yes"
+.BI "-[no]sumh" "yes "
average distance over equivalent hydrogens
-.TH g_rmsf 1 "Mon 29 Aug 2005"
+.TH g_rmsf 1 "Mon 22 Sep 2008"
.SH NAME
g_rmsf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "-f" " traj.xtc "
.BI "-[no]xvgr" ""
.BI "-[no]res" ""
.BI "-[no]aniso" ""
+.BI "-[no]fit" ""
.SH DESCRIPTION
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions
-after first fitting to a reference frame.
+after (optionally) fitting to a reference frame.
With option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]res" " no"
+.BI "-[no]res" "no "
Calculate averages for each residue
-.BI "-[no]aniso" " no"
+.BI "-[no]aniso" "no "
Compute anisotropic termperature factors
+.BI "-[no]fit" "yes "
+ Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.
+
-.TH g_rotacf 1 "Mon 29 Aug 2005"
+.TH g_rotacf 1 "Mon 22 Sep 2008"
.SH NAME
g_rotacf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use index doublets (vectors) for correlation function instead of triplets (planes)
-.BI "-[no]aver" " yes"
+.BI "-[no]aver" "yes "
Average over molecules
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_saltbr 1 "Mon 29 Aug 2005"
+.TH g_saltbr 1 "Mon 22 Sep 2008"
.SH NAME
g_saltbr
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "-f" " traj.xtc "
.BI "-t" " real "
.BI "-[no]sep" ""
.SH DESCRIPTION
-g_saltbr plots the difference between all combination of charged groups
+g_saltbr plots the distance between all combination of charged groups
as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg. the cut-off), then groups
that are never closer than that distance will not be plotted.
-Output will be in a number of fixed filenames, min-min.xvg,min-plus.xvg
+Output will be in a number of fixed filenames, min-min.xvg, plus-min.xvg
and plus-plus.xvg, or files for every individual ion-pair if selected
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-t" " real" " 1000"
+.BI "-t" " real" " 1000 "
trunc distance
-.BI "-[no]sep" " no"
+.BI "-[no]sep" "no "
Use separate files for each interaction (may be MANY)
-.TH g_sas 1 "Mon 29 Aug 2005"
+.TH g_sas 1 "Mon 22 Sep 2008"
.SH NAME
g_sas
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sas\fP
.BI "-f" " traj.xtc "
.BI "-o" " area.xvg "
.BI "-or" " resarea.xvg "
.BI "-oa" " atomarea.xvg "
+.BI "-tv" " volume.xvg "
.BI "-q" " connelly.pdb "
.BI "-n" " index.ndx "
.BI "-i" " surfat.itp "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
-.BI "-solsize" " real "
+.BI "-probe" " real "
.BI "-ndots" " int "
.BI "-qmax" " real "
.BI "-[no]f_index" ""
.BI "-minarea" " real "
-.BI "-[no]pbc" ""
.BI "-[no]prot" ""
.BI "-dgs" " real "
.SH DESCRIPTION
this can be turned off using the
.B -pbc
option.
+
+
+With the
+.B -tv
+option the total volume and density of the molecule can be
+computed.
+Please consider whether the normal probe radius is appropriate
+in this case or whether you would rather use e.g. 0. It is good
+to keep in mind that the results for volume and density are very
+approximate, in e.g. ice Ih one can easily fit water molecules in the
+pores which would yield too low volume, too high surface area and too
+high density.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " area.xvg"
.B Output
.B Output, Opt.
xvgr/xmgr file
+.BI "-tv" " volume.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-q" " connelly.pdb"
.B Output, Opt.
Protein data bank file
Include file for topology
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-solsize" " real" " 0.14"
+.BI "-probe" " real" " 0.14 "
Radius of the solvent probe (nm)
.BI "-ndots" " int" " 24"
Number of dots per sphere, more dots means more accuracy
-.BI "-qmax" " real" " 0.2"
+.BI "-qmax" " real" " 0.2 "
The maximum charge (e, absolute value) of a hydrophobic atom
-.BI "-[no]f_index" " no"
+.BI "-[no]f_index" "no "
Determine from a group in the index file what are the hydrophobic atoms rather than from the charge
-.BI "-minarea" " real" " 0.5"
+.BI "-minarea" " real" " 0.5 "
The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
-.BI "-[no]pbc" " yes"
- Take periodicity into account
-
-.BI "-[no]prot" " yes"
+.BI "-[no]prot" "yes "
Output the protein to the connelly pdb file too
-.BI "-dgs" " real" " 0"
+.BI "-dgs" " real" " 0 "
default value for solvation free energy per area (kJ/mol/nm2)
--- /dev/null
+.TH g_sdf 1 "Mon 22 Sep 2008"
+.SH NAME
+g_sdf
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_sdf\fP
+.BI "-f" " traj.xtc "
+.BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
+.BI "-o" " gom_plt.dat "
+.BI "-r" " refmol.gro "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-mode" " int "
+.BI "-triangle" " vector "
+.BI "-dtri" " vector "
+.BI "-bin" " real "
+.BI "-grid" " vector "
+.SH DESCRIPTION
+g_sdf calculates the spatial distribution function (SDF) of a set of atoms
+within a coordinate system defined by three atoms. There is single body,
+two body and three body SDF implemented (select with option -mode).
+In the single body case the local coordinate system is defined by using
+a triple of atoms from one single molecule, for the two and three body case
+the configurations are dynamically searched complexes of two or three
+molecules (or residues) meeting certain distance consitions (see below).
+
+
+The program needs a trajectory, a GROMACS run input file and an index
+file to work.
+You have to setup 4 groups in the index file before using g_sdf:
+
+
+The first three groups are used to define the SDF coordinate system.
+The programm will dynamically generate the atom tripels according to
+the selected -mode:
+In -mode 1 the triples will be just the 1st, 2nd, 3rd, ... atoms from
+groups 1, 2 and 3. Hence the nth entries in groups 1, 2 and 3 must be from the
+same residue. In -mode 2 the triples will be 1st, 2nd, 3rd, ... atoms from
+groups 1 and 2 (with the nth entries in groups 1 and 2 having the same res-id).
+For each pair from groups 1 and 2 group 3 is searched for an atom meeting the
+distance conditions set with -triangle and -dtri relative to atoms 1 and 2. In
+-mode 3 for each atom in group 1 group 2 is searched for an atom meeting the
+distance condition and if a pair is found group 3 is searched for an atom
+meeting the further conditions. The triple will only be used if all three atoms
+have different res-id's.
+
+
+The local coordinate system is always defined using the following scheme:
+Atom 1 will be used as the point of origin for the SDF. Atom 1 and 2 will define the principle axis (Z) of the coordinate system.
+The other two axis will be defined inplane (Y) and normal (X) to the plane through
+Atoms 1, 2 and 3. The fourth group
+contains the atoms for which the SDF will be evaluated.
+
+
+For -mode 2 and 3 you have to define the distance conditions for the
+2 resp. 3 molecule complexes to be searched for using -triangle and -dtri.
+
+
+The SDF will be sampled in cartesian coordinates.
+Use '-grid x y z' to define the size of the SDF grid around the
+reference molecule.
+The Volume of the SDF grid will be V=x*y*z (nm3). Use -bin to set the binwidth for grid.
+
+
+The output will be a binary 3D-grid file (gom_plt.dat) in the .plt format that can be be
+read directly by gOpenMol.
+The option -r will generate a .gro file with the reference molecule(s) transfered to
+the SDF coordinate system. Load this file into gOpenMol and display the
+SDF as a contour plot (see http://www.csc.fi/gopenmol/index.phtml for
+further documentation).
+
+
+For further information about SDF's have a look at: A. Vishnyakov, JPC A, 105,
+2001, 1702 and the references cited within.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-n" " index.ndx"
+.B Input
+ Index file
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-o" " gom_plt.dat"
+.B Output
+ Generic data file
+
+.BI "-r" " refmol.gro"
+.B Output, Opt.
+ Structure file: gro g96 pdb
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-mode" " int" " 1"
+ SDF in [1,2,3] particle mode
+
+.BI "-triangle" " vector" " 0 0 0"
+ r(1,3), r(2,3), r(1,2)
+
+.BI "-dtri" " vector" " 0.03 0.03 0.03"
+ dr(1,3), dr(2,3), dr(1,2)
+
+.BI "-bin" " real" " 0.05 "
+ Binwidth for the 3D-grid (nm)
+
+.BI "-grid" " vector" " 1 1 1"
+ Size of the 3D-grid (nm,nm,nm)
+
-.TH g_sgangle 1 "Mon 29 Aug 2005"
+.TH g_sgangle 1 "Mon 22 Sep 2008"
.SH NAME
g_sgangle
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
-.BI "-[no]pbc" ""
.BI "-[no]one" ""
.BI "-[no]z" ""
.SH DESCRIPTION
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-oa" " sg_angle.xvg"
.B Output
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]pbc" " no"
- Use periodic boundary conditions
-
-.BI "-[no]one" " no"
+.BI "-[no]one" "no "
Only one group compute angle between vector at time zero and time t
-.BI "-[no]z" " no"
+.BI "-[no]z" "no "
Use the Z-axis as reference
-.TH g_sham 1 "Mon 29 Aug 2005"
+.TH g_sham 1 "Mon 22 Sep 2008"
.SH NAME
g_sham
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sham\fP
.BI "-f" " graph.xvg "
.BI "-dist" " ener.xvg "
.BI "-histo" " edist.xvg "
.BI "-bin" " bindex.ndx "
+.BI "-lp" " prob.xpm "
.BI "-ls" " gibbs.xpm "
.BI "-lsh" " enthalpy.xpm "
.BI "-lss" " entropy.xpm "
.BI "-ngrid" " vector "
.BI "-xmin" " vector "
.BI "-xmax" " vector "
+.BI "-pmax" " real "
.BI "-gmax" " real "
+.BI "-emin" " real "
+.BI "-emax" " real "
.BI "-nlevels" " int "
.BI "-mname" " string "
.SH DESCRIPTION
-g_sham reads a number of xvg files and analyzes data sets.
+g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
+g_sham reads one or more xvg files and analyzes data sets.
+g_sham basic purpose is plotting Gibbs free energy landscapes
+(option
+.B -ls
+)
+by Bolzmann inverting multi-dimensional histograms (option
+.B -lp
+)
+but it can also
+make enthalpy (option
+.B -lsh
+) and entropy (option
+.B -lss
+)
+plots. The histograms can be made for any quantities the user supplies.
A line in the input file may start with a time
(see option
.B -time
Option
.B -ge
can be used to supply a file with free energies
-when the ensemble is not a Boltzmann ensemble, but has been biased
-by this free energy.
+when the ensemble is not a Boltzmann ensemble, but needs to be biased
+by this free energy. One free energy value is required for each
+(multi-dimensional) data point in the
+.B -f
+input.
+
+
+
+Option
+.B -ene
+can be used to supply a file with energies.
+These energies are used as a weighting function in the single
+histogram analysis method due to Kumar et. al. When also temperatures
+are supplied (as a second column in the file) an experimental
+weighting scheme is applied. In addition the vales
+are used for making enthalpy and entropy plots.
When a distance is 2- or 3-dimensional, the circumference or surface
sampled by two particles increases with increasing distance.
Depending on what one would like to show, one can choose to correct
-the free-energy for this volume effect.
+the histogram and free-energy for this volume effect.
The probability is normalized by r and r2 for a dimension of 2 and 3
respectively.
+A value of -1 is used to indicate an angle in degrees between two
+vectors: a sin(angle) normalization will be applied.
Note that for angles between vectors the inner-product or cosine
is the natural quantity to use, as it will produce bins of the same
volume.
.B Output, Opt.
Index file
+.BI "-lp" " prob.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.BI "-ls" " gibbs.xpm"
.B Output, Opt.
X PixMap compatible matrix file
Log file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]time" " yes"
+.BI "-[no]time" "yes "
Expect a time in the input
-.BI "-b" " real" " -1"
+.BI "-b" " real" " -1 "
First time to read from set
-.BI "-e" " real" " -1"
+.BI "-e" " real" " -1 "
Last time to read from set
-.BI "-ttol" " real" " 0"
+.BI "-ttol" " real" " 0 "
Tolerance on time in appropriate units (usually ps)
.BI "-n" " int" " 1"
Read sets seperated by &
-.BI "-[no]d" " no"
+.BI "-[no]d" "no "
Use the derivative
-.BI "-bw" " real" " 0.1"
+.BI "-bw" " real" " 0.1 "
Binwidth for the distribution
-.BI "-[no]sham" " yes"
+.BI "-[no]sham" "yes "
Turn off energy weighting even if energies are given
.BI "-tsham" " real" " 298.15"
Temperature for single histogram analysis
-.BI "-pmin" " real" " 0"
+.BI "-pmin" " real" " 0 "
Minimum probability. Anything lower than this will be set to zero
.BI "-dim" " vector" " 1 1 1"
.BI "-xmax" " vector" " 1 1 1"
Maximum for the axes in energy landscape (see above for 3 dimensions)
-.BI "-gmax" " real" " 0"
- Maximum level in output, 0 is calculate
+.BI "-pmax" " real" " 0 "
+ Maximum probability in output, default is calculate
+
+.BI "-gmax" " real" " 0 "
+ Maximum free energy in output, default is calculate
+
+.BI "-emin" " real" " 0 "
+ Minimum enthalpy in output, default is calculate
+
+.BI "-emax" " real" " 0 "
+ Maximum enthalpy in output, default is calculate
.BI "-nlevels" " int" " 25"
- Number of levels for energy landscape from single histogram analysis
+ Number of levels for energy landscape
.BI "-mname" " string" " "
Legend label for the custom landscape
-.TH g_sorient 1 "Mon 29 Aug 2005"
+.TH g_sorient 1 "Mon 22 Sep 2008"
.SH NAME
g_sorient
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_sorient\fP
.BI "-f" " traj.xtc "
.BI "-no" " snor.xvg "
.BI "-ro" " sord.xvg "
.BI "-co" " scum.xvg "
+.BI "-rc" " scount.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
.BI "-[no]com" ""
+.BI "-[no]v23" ""
.BI "-rmin" " real "
.BI "-rmax" " real "
-.BI "-bin" " real "
+.BI "-cbin" " real "
+.BI "-rbin" " real "
.BI "-[no]pbc" ""
.SH DESCRIPTION
g_sorient analyzes solvent orientation around solutes.
molecule to the midpoint between atoms 2 and 3.
theta2: the angle with the normal of the solvent plane, defined by the
-same three atoms.
+same three atoms, or when the option
+.B -v23
+is set
+the angle with the vector between atoms 2 and 3.
The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
.B -no
-: distribution of 3cos2(theta2)-1 for rmin=r=rmax.
+: distribution of cos(theta2) for rmin=r=rmax.
of cos(theta1) and 3cos2(theta2)-1 as a function of r.
+
+.B -rc
+: the distribution of the solvent molecules as a function of r
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output
xvgr/xmgr file
+.BI "-rc" " scount.xvg"
+.B Output
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Use the center of mass as the reference postion
-.BI "-rmin" " real" " 0"
- Minimum distance
+.BI "-[no]v23" "no "
+ Use the vector between atoms 2 and 3
+
+.BI "-rmin" " real" " 0 "
+ Minimum distance (nm)
+
+.BI "-rmax" " real" " 0.5 "
+ Maximum distance (nm)
-.BI "-rmax" " real" " 0.5"
- Maximum distance
+.BI "-cbin" " real" " 0.02 "
+ Binwidth for the cosine
-.BI "-bin" " real" " 0.02"
- Binwidth
+.BI "-rbin" " real" " 0.02 "
+ Binwidth for r (nm)
-.BI "-[no]pbc" " no"
+.BI "-[no]pbc" "no "
Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.
--- /dev/null
+.TH g_spatial 1 "Mon 22 Sep 2008"
+.SH NAME
+g_spatial
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_spatial\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-dm" " rmsd.xpm "
+.BI "-o" " rmsd-clust.xpm "
+.BI "-g" " cluster.log "
+.BI "-dist" " rmsd-dist.xvg "
+.BI "-ev" " rmsd-eig.xvg "
+.BI "-sz" " clust-size.xvg "
+.BI "-tr" " clust-trans.xpm "
+.BI "-ntr" " clust-trans.xvg "
+.BI "-clid" " clust-id.xvg "
+.BI "-cl" " clusters.pdb "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-tu" " enum "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-[no]dista" ""
+.BI "-nlevels" " int "
+.BI "-cutoff" " real "
+.BI "-[no]fit" ""
+.BI "-max" " real "
+.BI "-skip" " int "
+.BI "-[no]av" ""
+.BI "-wcl" " int "
+.BI "-nst" " int "
+.BI "-rmsmin" " real "
+.BI "-method" " enum "
+.BI "-minstruct" " int "
+.BI "-[no]binary" ""
+.BI "-M" " int "
+.BI "-P" " int "
+.BI "-seed" " int "
+.BI "-niter" " int "
+.BI "-kT" " real "
+.SH DESCRIPTION
+g_cluster can cluster structures with several different methods.
+Distances between structures can be determined from a trajectory
+or read from an XPM matrix file with the
+.B -dm
+option.
+RMS deviation after fitting or RMS deviation of atom-pair distances
+can be used to define the distance between structures.
+
+
+single linkage: add a structure to a cluster when its distance to any
+element of the cluster is less than
+.B cutoff
+.
+
+
+Jarvis Patrick: add a structure to a cluster when this structure
+and a structure in the cluster have each other as neighbors and
+they have a least
+.B P
+neighbors in common. The neighbors
+of a structure are the M closest structures or all structures within
+
+.B cutoff
+.
+
+
+Monte Carlo: reorder the RMSD matrix using Monte Carlo.
+
+
+diagonalization: diagonalize the RMSD matrix.
+
+gromos: use algorithm as described in Daura
+.I et al.
+
+(
+.I Angew. Chem. Int. Ed.
+
+.B 1999
+,
+.I 38
+, pp 236-240).
+Count number of neighbors using cut-off, take structure with
+largest number of neighbors with all its neighbors as cluster
+and eleminate it from the pool of clusters. Repeat for remaining
+structures in pool.
+
+
+When the clustering algorithm assigns each structure to exactly one
+cluster (single linkage, Jarvis Patrick and gromos) and a trajectory
+file is supplied, the structure with
+the smallest average distance to the others or the average structure
+or all structures for each cluster will be written to a trajectory
+file. When writing all structures, separate numbered files are made
+for each cluster.
+
+Two output files are always written:
+
+
+.B -o
+writes the RMSD values in the upper left half of the matrix
+and a graphical depiction of the clusters in the lower right half
+When
+.B -minstruct
+= 1 the graphical depiction is black
+when two structures are in the same cluster.
+When
+.B -minstruct
+ 1 different colors will be used for each
+cluster.
+
+
+.B -g
+writes information on the options used and a detailed list
+of all clusters and their members.
+
+
+Additionally, a number of optional output files can be written:
+
+
+.B -dist
+writes the RMSD distribution.
+
+
+.B -ev
+writes the eigenvectors of the RMSD matrix
+diagonalization.
+
+
+.B -sz
+writes the cluster sizes.
+
+
+.B -tr
+writes a matrix of the number transitions between
+cluster pairs.
+
+
+.B -ntr
+writes the total number of transitions to or from
+each cluster.
+
+
+.B -clid
+writes the cluster number as a function of time.
+
+
+.B -cl
+writes average (with option
+.B -av
+) or central
+structure of each cluster or writes numbered files with cluster members
+for a selected set of clusters (with option
+.B -wcl
+, depends on
+
+.B -nst
+and
+.B -rmsmin
+).
+
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input, Opt.
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-s" " topol.tpr"
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-dm" " rmsd.xpm"
+.B Input, Opt.
+ X PixMap compatible matrix file
+
+.BI "-o" " rmsd-clust.xpm"
+.B Output
+ X PixMap compatible matrix file
+
+.BI "-g" " cluster.log"
+.B Output
+ Log file
+
+.BI "-dist" " rmsd-dist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ev" " rmsd-eig.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-sz" " clust-size.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-tr" " clust-trans.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-ntr" " clust-trans.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-clid" " clust-id.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-cl" " clusters.pdb"
+.B Output, Opt.
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-tu" " enum" " ps"
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+or
+.B s
+
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-[no]dista" "no "
+ Use RMSD of distances instead of RMS deviation
+
+.BI "-nlevels" " int" " 40"
+ Discretize RMSD matrix in levels
+
+.BI "-cutoff" " real" " 0.1 "
+ RMSD cut-off (nm) for two structures to be neighbor
+
+.BI "-[no]fit" "yes "
+ Use least squares fitting before RMSD calculation
+
+.BI "-max" " real" " -1 "
+ Maximum level in RMSD matrix
+
+.BI "-skip" " int" " 1"
+ Only analyze every nr-th frame
+
+.BI "-[no]av" "no "
+ Write average iso middle structure for each cluster
+
+.BI "-wcl" " int" " 0"
+ Write all structures for first clusters to numbered files
+
+.BI "-nst" " int" " 1"
+ Only write all structures if more than per cluster
+
+.BI "-rmsmin" " real" " 0 "
+ minimum rms difference with rest of cluster for writing structures
+
+.BI "-method" " enum" " linkage"
+ Method for cluster determination:
+.B linkage
+,
+.B jarvis-patrick
+,
+.B monte-carlo
+,
+.B diagonalization
+or
+.B gromos
+
+
+.BI "-minstruct" " int" " 1"
+ Minimum number of structures in cluster for coloring in the xpm file
+
+.BI "-[no]binary" "no "
+ Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
+
+.BI "-M" " int" " 10"
+ Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff
+
+.BI "-P" " int" " 3"
+ Number of identical nearest neighbors required to form a cluster
+
+.BI "-seed" " int" " 1993"
+ Random number seed for Monte Carlo clustering algorithm
+
+.BI "-niter" " int" " 10000"
+ Number of iterations for MC
+
+.BI "-kT" " real" " 0.001 "
+ Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps)
+
--- /dev/null
+.TH g_spol 1 "Mon 22 Sep 2008"
+.SH NAME
+g_spol
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_spol\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-o" " scdist.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-[no]com" ""
+.BI "-refat" " int "
+.BI "-rmin" " real "
+.BI "-rmax" " real "
+.BI "-dip" " real "
+.BI "-bw" " real "
+.SH DESCRIPTION
+g_spol analyzes dipoles around a solute; it is especially useful
+for polarizable water. A group of reference atoms, or a center
+of mass reference (option
+.B -com
+) and a group of solvent
+atoms is required. The program splits the group of solvent atoms
+into molecules. For each solvent molecule the distance to the
+closest atom in reference group or to the COM is determined.
+A cumulative distribution of these distances is plotted.
+For each distance between
+.B -rmin
+and
+.B -rmax
+
+the inner product of the distance vector
+and the dipole of the solvent molecule is determined.
+The average of these dipole components is printed.
+The same is done for the polarization, where the average dipole is
+subtracted from the instantaneous dipole. The magnitude of the average
+dipole is set with the option
+.B -dip
+, the direction is defined
+by the vector from the first atom in the selected solvent group
+to the midpoint between the second and the third atom.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-s" " topol.tpr"
+.B Input
+ Run input file: tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " scdist.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-[no]com" "no "
+ Use the center of mass as the reference postion
+
+.BI "-refat" " int" " 1"
+ The reference atom of the solvent molecule
+
+.BI "-rmin" " real" " 0 "
+ Maximum distance (nm)
+
+.BI "-rmax" " real" " 0.32 "
+ Maximum distance (nm)
+
+.BI "-dip" " real" " 0 "
+ The average dipole (D)
+
+.BI "-bw" " real" " 0.01 "
+ The bin width
+
-.TH g_tcaf 1 "Mon 29 Aug 2005"
+.TH g_tcaf 1 "Mon 22 Sep 2008"
.SH NAME
g_tcaf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "-f" " traj.trr "
.SH FILES
.BI "-f" " traj.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Calculate tcaf of molecules
-.BI "-[no]k34" " no"
+.BI "-[no]k34" "no "
Also use k=(3,0,0) and k=(4,0,0)
-.BI "-wt" " real" " 5"
+.BI "-wt" " real" " 5 "
Exponential decay time for the TCAF fit weights
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_traj 1 "Mon 29 Aug 2005"
+.TH g_traj 1 "Mon 22 Sep 2008"
.SH NAME
g_traj
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_traj\fP
.BI "-f" " traj.xtc "
.BI "-s" " topol.tpr "
.BI "-n" " index.ndx "
.BI "-ox" " coord.xvg "
+.BI "-oxt" " coord.xtc "
.BI "-ov" " veloc.xvg "
.BI "-of" " force.xvg "
.BI "-ob" " box.xvg "
.BI "-vd" " veldist.xvg "
.BI "-cv" " veloc.pdb "
.BI "-cf" " force.pdb "
+.BI "-av" " all_veloc.xvg "
+.BI "-af" " all_force.xvg "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-b" " time "
the
.B -nojump
option to obtain the correct average coordinates.
+If you select either of these option the average force and velocity
+for each atom are written to an xvg file as well
+(specified with
+.B -av
+or
+.B -af
+).
Option
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.B Output, Opt.
xvgr/xmgr file
+.BI "-oxt" " coord.xtc"
+.B Output, Opt.
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
.BI "-ov" " veloc.xvg"
.B Output, Opt.
xvgr/xmgr file
.B Output, Opt.
Protein data bank file
+.BI "-av" " all_veloc.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-af" " all_force.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Plot data for the com of each group
-.BI "-[no]mol" " no"
+.BI "-[no]mol" "no "
Index contains molecule numbers iso atom numbers
-.BI "-[no]nojump" " no"
+.BI "-[no]nojump" "no "
Remove jumps of atoms across the box
-.BI "-[no]x" " yes"
+.BI "-[no]x" "yes "
Plot X-component
-.BI "-[no]y" " yes"
+.BI "-[no]y" "yes "
Plot Y-component
-.BI "-[no]z" " yes"
+.BI "-[no]z" "yes "
Plot Z-component
.BI "-ng" " int" " 1"
Number of groups to consider
-.BI "-[no]len" " no"
+.BI "-[no]len" "no "
Plot vector length
-.BI "-bin" " real" " 1"
+.BI "-bin" " real" " 1 "
Binwidth for velocity histogram (nm/ps)
-.BI "-scale" " real" " 0"
+.BI "-scale" " real" " 0 "
Scale factor for pdb output, 0 is autoscale
--- /dev/null
+.TH g_vanhove 1 "Mon 22 Sep 2008"
+.SH NAME
+g_vanhove
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3g_vanhove\fP
+.BI "-f" " traj.xtc "
+.BI "-s" " topol.tpr "
+.BI "-n" " index.ndx "
+.BI "-om" " vanhove.xpm "
+.BI "-or" " vanhove_r.xvg "
+.BI "-ot" " vanhove_t.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-sqrt" " real "
+.BI "-fm" " int "
+.BI "-rmax" " real "
+.BI "-rbin" " real "
+.BI "-mmax" " real "
+.BI "-nlevels" " int "
+.BI "-nr" " int "
+.BI "-fr" " int "
+.BI "-rt" " real "
+.BI "-ft" " int "
+.SH DESCRIPTION
+g_vanhove computes the Van Hove correlation function.
+The Van Hove G(r,t) is the probability that a particle that is at r0
+at time zero can be found at position r0+r at time t.
+g_vanhove determines G not for a vector r, but for the length of r.
+Thus it gives the probability that a particle moves a distance of r
+in time t.
+Jumps across the periodic boundaries are removed.
+Corrections are made for scaling due to isotropic
+or anisotropic pressure coupling.
+
+
+
+With option
+.B -om
+the whole matrix can be written as a function
+of t and r or as a function of sqrt(t) and r (option
+.B -sqrt
+).
+
+
+
+With option
+.B -or
+the Van Hove function is plotted for one
+or more values of t. Option
+.B -nr
+sets the number of times,
+option
+.B -fr
+the number spacing between the times.
+The binwidth is set with option
+.B -rbin
+. The number of bins
+is determined automatically.
+
+
+
+With option
+.B -ot
+the integral up to a certain distance
+(option
+.B -rt
+) is plotted as a function of time.
+
+
+
+For all frames that are read the coordinates of the selected particles
+are stored in memory. Therefore the program may use a lot of memory.
+For options
+.B -om
+and
+.B -ot
+the program may be slow.
+This is because the calculation scales as the number of frames times
+
+.B -fm
+or
+.B -ft
+.
+Note that with the
+.B -dt
+option the memory usage and calculation
+time can be reduced.
+.SH FILES
+.BI "-f" " traj.xtc"
+.B Input
+ Trajectory: xtc trr trj gro g96 pdb cpt
+
+.BI "-s" " topol.tpr"
+.B Input
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-om" " vanhove.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-or" " vanhove_r.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.BI "-ot" " vanhove_t.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 19"
+ Set the nicelevel
+
+.BI "-b" " time" " 0 "
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " 0 "
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " 0 "
+ Only use frame when t MOD dt = first time (ps)
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-sqrt" " real" " 0 "
+ Use sqrt(t) on the matrix axis which binspacing in sqrt(ps)
+
+.BI "-fm" " int" " 0"
+ Number of frames in the matrix, 0 is plot all
+
+.BI "-rmax" " real" " 2 "
+ Maximum r in the matrix (nm)
+
+.BI "-rbin" " real" " 0.01 "
+ Binwidth in the matrix and for -or (nm)
+
+.BI "-mmax" " real" " 0 "
+ Maximum density in the matrix, 0 is calculate (1/nm)
+
+.BI "-nlevels" " int" " 81"
+ Number of levels in the matrix
+
+.BI "-nr" " int" " 1"
+ Number of curves for the -or output
+
+.BI "-fr" " int" " 0"
+ Frame spacing for the -or output
+
+.BI "-rt" " real" " 0 "
+ Integration limit for the -ot output (nm)
+
+.BI "-ft" " int" " 0"
+ Number of frames in the -ot output, 0 is plot all
+
-.TH g_velacc 1 "Mon 29 Aug 2005"
+.TH g_velacc 1 "Mon 22 Sep 2008"
.SH NAME
g_velacc
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_velacc\fP
.BI "-f" " traj.trr "
.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-[no]xvgr" ""
+.BI "-[no]m" ""
.BI "-[no]mol" ""
.BI "-acflen" " int "
.BI "-[no]normalize" ""
.SH DESCRIPTION
g_velacc computes the velocity autocorrelation function.
When the
-.B -s
+.B -m
option is used, the momentum autocorrelation
function is calculated.
.SH FILES
.BI "-f" " traj.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-[no]mol" " no"
- Calculate vac of molecules
+.BI "-[no]m" "no "
+ Calculate the momentum autocorrelation function
+
+.BI "-[no]mol" "no "
+ Calculate the momentum acf of molecules
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.BI "-[no]normalize" " yes"
+.BI "-[no]normalize" "yes "
Normalize ACF
.BI "-P" " enum" " 0"
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.BI "-beginfit" " real" " 0"
+.BI "-beginfit" " real" " 0 "
Time where to begin the exponential fit of the correlation function
-.BI "-endfit" " real" " -1"
+.BI "-endfit" " real" " -1 "
Time where to end the exponential fit of the correlation function, -1 is till the end
-.TH g_wham 1 "Mon 29 Aug 2005"
+.TH g_wham 1 "Mon 22 Sep 2008"
.SH NAME
g_wham
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3g_wham\fP
.BI "-o" " profile.xvg "
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-min" " real" " 0"
+.BI "-min" " real" " 0 "
Minimum coordinate in profile
-.BI "-max" " real" " 0"
+.BI "-max" " real" " 0 "
Maximum coordinate in profile
.BI "-bins" " int" " 100"
Number of bins in profile
-.BI "-[no]prof" " yes"
+.BI "-[no]prof" "yes "
Only calculate min and max
-.BI "-temp" " real" " 298"
+.BI "-temp" " real" " 298 "
Temperature
-.BI "-[no]flip" " no"
+.BI "-[no]flip" "no "
Combine halves of profile
-.BI "-tol" " real" " 0.01"
+.BI "-tol" " real" " 0.01 "
Tolerance
-.TH genbox 1 "Mon 29 Aug 2005"
+.TH genbox 1 "Mon 22 Sep 2008"
.SH NAME
genbox
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genbox\fP
.BI "-cp" " protein.gro "
.BI "-seed" " int "
.BI "-vdwd" " real "
.BI "-shell" " real "
+.BI "-maxsol" " int "
+.BI "-[no]vel" ""
.SH DESCRIPTION
Genbox can do one of 3 things:
) is used,
unless
.B -box
-is set, which also centers the solute.
-The program
+is set.
+If you want the solute to be centered in the box,
+the program
.B editconf
-has more sophisticated options to change
-the box and center the solute.
+has sophisticated options
+to change the box dimensions and center the solute.
Solvent molecules are removed from the box where the
distance between any atom of the solute molecule(s) and any atom of
the solvent molecule is less than the sum of the VanderWaals radii of
.SH FILES
.BI "-cp" " protein.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-cs" " spc216.gro"
.B Input, Opt., Lib.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-ci" " insert.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-p" " topol.top"
.B In/Out, Opt.
Topology file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-seed" " int" " 1997"
random generator seed
-.BI "-vdwd" " real" " 0.105"
+.BI "-vdwd" " real" " 0.105 "
default vdwaals distance
-.BI "-shell" " real" " 0"
+.BI "-shell" " real" " 0 "
thickness of optional water layer around solute
-\- Molecules must be whole in the initial configurations.
+.BI "-maxsol" " int" " 0"
+ maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored
+
+.BI "-[no]vel" "no "
+ keep velocities from input solute and solvent
-\- At the moment -ci only works when inserting one molecule.
+.SH KNOWN PROBLEMS
+\- Molecules must be whole in the initial configurations.
-.TH genconf 1 "Mon 29 Aug 2005"
+.TH genconf 1 "Mon 22 Sep 2008"
.SH NAME
genconf
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genconf\fP
.BI "-f" " conf.gro "
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-trj" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
.BI "-seed" " int" " 0"
Random generator seed, if 0 generated from the time
-.BI "-[no]rot" " no"
+.BI "-[no]rot" "no "
Randomly rotate conformations
-.BI "-[no]shuffle" " no"
+.BI "-[no]shuffle" "no "
Random shuffling of molecules
-.BI "-[no]sort" " no"
+.BI "-[no]sort" "no "
Sort molecules on X coord
.BI "-block" " int" " 1"
.BI "-maxrot" " vector" " 90 90 90"
Maximum random rotation
-.BI "-[no]renumber" " yes"
+.BI "-[no]renumber" "yes "
Renumber residues
+.SH KNOWN PROBLEMS
\- The program should allow for random displacement off lattice points.
-.TH genion 1 "Mon 29 Aug 2005"
+.TH genion 1 "Mon 22 Sep 2008"
.SH NAME
genion
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3genion\fP
.BI "-s" " topol.tpr "
.BI "-o" " out.gro "
.BI "-g" " genion.log "
.BI "-pot" " pot.pdb "
+.BI "-p" " topol.top "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]xvgr" ""
.BI "-np" " int "
.BI "-pname" " string "
-.BI "-pq" " real "
+.BI "-pq" " int "
.BI "-nn" " int "
.BI "-nname" " string "
-.BI "-nq" " real "
+.BI "-nq" " int "
.BI "-rmin" " real "
.BI "-[no]random" ""
.BI "-seed" " int "
.BI "-scale" " real "
+.BI "-conc" " real "
+.BI "-[no]neutral" ""
.SH DESCRIPTION
genion replaces solvent molecules by monoatomic ions at
the position of the first atoms with the most favorable electrostatic
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-table" " table.xvg"
.B Input, Opt.
.BI "-o" " out.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-g" " genion.log"
.B Output
.B Output, Opt.
Protein data bank file
+.BI "-p" " topol.top"
+.B In/Out, Opt.
+ Topology file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-np" " int" " 0"
.BI "-pname" " string" " Na"
Name of the positive ion
-.BI "-pq" " real" " 1"
+.BI "-pq" " int" " 1"
Charge of the positive ion
.BI "-nn" " int" " 0"
.BI "-nname" " string" " Cl"
Name of the negative ion
-.BI "-nq" " real" " -1"
+.BI "-nq" " int" " -1"
Charge of the negative ion
-.BI "-rmin" " real" " 0.6"
+.BI "-rmin" " real" " 0.6 "
Minimum distance between ions
-.BI "-[no]random" " no"
+.BI "-[no]random" "yes "
Use random placement of ions instead of based on potential. The rmin option should still work
.BI "-seed" " int" " 1993"
Seed for random number generator
-.BI "-scale" " real" " 0.001"
+.BI "-scale" " real" " 0.001 "
Scaling factor for the potential for -pot
+.BI "-conc" " real" " 0 "
+ Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input tpr file. Overrides the -np and nn options.
+
+.BI "-[no]neutral" "no "
+ This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated.
+
+.SH KNOWN PROBLEMS
+\- Calculation of the potential is not reliable, therefore the
+.B -random
+option is now turned on by default.
+
+\- If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.
+
--- /dev/null
+.TH genrestr 1 "Mon 22 Sep 2008"
+.SH NAME
+genrestr
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3genrestr\fP
+.BI "-f" " conf.gro "
+.BI "-n" " index.ndx "
+.BI "-o" " posre.itp "
+.BI "-of" " freeze.ndx "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-fc" " vector "
+.BI "-freeze" " real "
+.BI "-[no]disre" ""
+.BI "-disre_dist" " real "
+.BI "-disre_frac" " real "
+.BI "-disre_up2" " real "
+.BI "-[no]constr" ""
+.SH DESCRIPTION
+genrestr produces an include file for a topology containing
+a list of atom numbers and three force constants for the
+X, Y and Z direction. A single isotropic force constant may
+be given on the command line instead of three components.
+
+
+WARNING: position restraints only work for the one molecule at a time.
+Position restraints are interactions within molecules, therefore
+they should be included within the correct
+.B [ moleculetype ]
+
+block in the topology. Since the atom numbers in every moleculetype
+in the topology start at 1 and the numbers in the input file for
+genpr number consecutively from 1, genpr will only produce a useful
+file for the first molecule.
+
+
+The -of option produces an index file that can be used for
+freezing atoms. In this case the input file must be a pdb file.
+
+
+With the
+.B -disre
+option half a matrix of distance restraints
+is generated instead of position restraints. With this matrix, that
+one typically would apply to C-alpha atoms in a protein, one can
+maintain the overall conformation of a protein without tieing it to
+a specific position (as with position restraints).
+.SH FILES
+.BI "-f" " conf.gro"
+.B Input
+ Structure file: gro g96 pdb tpr tpb tpa
+
+.BI "-n" " index.ndx"
+.B Input, Opt.
+ Index file
+
+.BI "-o" " posre.itp"
+.B Output
+ Include file for topology
+
+.BI "-of" " freeze.ndx"
+.B Output, Opt.
+ Index file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-fc" " vector" " 1000 1000 1000"
+ force constants (kJ mol-1 nm-2)
+
+.BI "-freeze" " real" " 0 "
+ if the -of option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here
+
+.BI "-[no]disre" "no "
+ Generate a distance restraint matrix for all the atoms in index
+
+.BI "-disre_dist" " real" " 0.1 "
+ Distance range around the actual distance for generating distance restraints
+
+.BI "-disre_frac" " real" " 0 "
+ Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead.
+
+.BI "-disre_up2" " real" " 1 "
+ Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)
+
+.BI "-[no]constr" "no "
+ Generate a constraint matrix rather than distance restraints
+
-.TH gmxcheck 1 "Mon 29 Aug 2005"
+.TH gmxcheck 1 "Mon 22 Sep 2008"
.SH NAME
gmxcheck
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
.BI "-e2" " ener2.edr "
.BI "-n" " index.ndx "
+.BI "-m" " doc.tex "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-vdwfac" " real "
.BI "-bonlo" " real "
.BI "-bonhi" " real "
.BI "-tol" " real "
+.BI "-[no]ab" ""
.BI "-lastener" " string "
.SH DESCRIPTION
gmxcheck reads a trajectory (
or
.B .xtc
-) or an energy file (
+), an energy file (
.B .ene
or
.B .edr
)
+or an index file (
+.B .ndx
+)
and prints out useful information about them.
option), or a pair of energy files (using the
.B -e2
option).
+
+
+For free energy simulations the A and B state topology from one
+run input file can be compared with options
+.B -s1
+and
+.B -ab
+.
+
+
+In case the
+.B -m
+flag is given a LaTeX file will be written
+consisting a rough outline for a methods section for a paper.
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-f2" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s1" " top1.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-s2" " top2.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-c" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-e2" " ener2.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
+.BI "-m" " doc.tex"
+.B Output, Opt.
+ LaTeX file
+
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-vdwfac" " real" " 0.8"
+.BI "-vdwfac" " real" " 0.8 "
Fraction of sum of VdW radii used as warning cutoff
-.BI "-bonlo" " real" " 0.4"
+.BI "-bonlo" " real" " 0.4 "
Min. fract. of sum of VdW radii for bonded atoms
-.BI "-bonhi" " real" " 0.7"
+.BI "-bonhi" " real" " 0.7 "
Max. fract. of sum of VdW radii for bonded atoms
-.BI "-tol" " real" " 0.001"
+.BI "-tol" " real" " 0.001 "
Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
+.BI "-[no]ab" "no "
+ Compare the A and B topology from one file
+
.BI "-lastener" " string" " "
Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
-.TH gmxdump 1 "Mon 29 Aug 2005"
+.TH gmxdump 1 "Mon 22 Sep 2008"
.SH NAME
gmxdump
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3gmxdump\fP
.BI "-s" " topol.tpr "
.BI "-f" " traj.xtc "
.BI "-e" " ener.edr "
+.BI "-cp" " state.cpt "
+.BI "-om" " grompp.mdp "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-[no]nr" ""
checking your run input file in case of problems.
+When requesting to dump a topology file the program will dump
+the processed topology, since not all original information is maintained
+in tpr files.
.SH FILES
.BI "-s" " topol.tpr"
.B Input, Opt.
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
+
+.BI "-cp" " state.cpt"
+.B Input, Opt.
+ Checkpoint file
+
+.BI "-om" " grompp.mdp"
+.B Output, Opt.
+ grompp input file with MD parameters
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]nr" " yes"
+.BI "-[no]nr" "yes "
Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
-.TH grompp 1 "Mon 29 Aug 2005"
+.TH grompp 1 "Mon 22 Sep 2008"
.SH NAME
grompp
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3grompp\fP
.BI "-f" " grompp.mdp "
.BI "-r" " conf.gro "
.BI "-rb" " conf.gro "
.BI "-n" " index.ndx "
-.BI "-deshuf" " deshuf.ndx "
.BI "-p" " topol.top "
.BI "-pp" " processed.top "
.BI "-o" " topol.tpr "
.BI "-nice" " int "
.BI "-[no]v" ""
.BI "-time" " real "
-.BI "-np" " int "
-.BI "-[no]shuffle" ""
-.BI "-[no]sort" ""
.BI "-[no]rmvsbds" ""
-.BI "-load" " string "
.BI "-maxwarn" " int "
-.BI "-[no]check14" ""
+.BI "-[no]zero" ""
.BI "-[no]renum" ""
.SH DESCRIPTION
The gromacs preprocessor
only the atom types are used for generating interaction parameters.
-grompp calls the c-preprocessor to resolve includes, macros
-etcetera. To specify a macro-preprocessor other than /lib/cpp
-(such as m4)
+grompp calls a preprocessor to resolve includes, macros
+etcetera. By default we use the cpp in your path. To specify a different macro-preprocessor (e.g. m4) or alternative location
you can put a line in your parameter file specifying the path
-to that cpp. Specifying
+to that program. Specifying
.B -pp
will get the pre-processed
topology file written out.
.
-When preparing an input file for parallel
-.B mdrun
-it may
-be advantageous to partition the simulation system over the
-nodes in a way in which each node has a similar amount of
-work. The -shuffle option does just that. For a single protein
-in water this does not make a difference, however for a system where
-you have many copies of different molecules (e.g. liquid mixture
-or membrane/water system) the option is definitely a must.
-The output trajectories will also be shuffled.
-.B grompp
-writes
-an index file (option
-.B -deshuf
-) which can be used with
-
-.B trjconv
-to deshuffle the trajectories.
-
-
-A further optimization for parallel systems is the
-.B -sort
-
-option which sorts molecules according to coordinates. This must
-always be used in conjunction with
-.B -shuffle
-, however
-sorting also works when you have only one molecule type.
-
-
Using the
.B -morse
option grompp can convert the harmonic bonds
.BI "-c" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-r" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-rb" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
-.BI "-deshuf" " deshuf.ndx"
-.B Output, Opt.
- Index file
-
.BI "-p" " topol.top"
.B Input
Topology file
.BI "-o" " topol.tpr"
.B Output
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-t" " traj.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]v" " yes"
+.BI "-[no]v" "yes "
Be loud and noisy
-.BI "-time" " real" " -1"
+.BI "-time" " real" " -1 "
Take frame at or first after this time.
-.BI "-np" " int" " 1"
- Generate statusfile for nodes
-
-.BI "-[no]shuffle" " no"
- Shuffle molecules over nodes
-
-.BI "-[no]sort" " no"
- Sort molecules according to X coordinate
-
-.BI "-[no]rmvsbds" " yes"
+.BI "-[no]rmvsbds" "yes "
Remove constant bonded interactions with virtual sites
-.BI "-load" " string" " "
- Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node
-
-.BI "-maxwarn" " int" " 10"
- Number of warnings after which input processing stops
+.BI "-maxwarn" " int" " 0"
+ Number of allowed warnings during input processing
-.BI "-[no]check14" " no"
- Remove 1-4 interactions without Van der Waals
+.BI "-[no]zero" "no "
+ Set parameters for bonded interactions without defaults to zero instead of generating an error
-.BI "-[no]renum" " yes"
+.BI "-[no]renum" "yes "
Renumber atomtypes and minimize number of atomtypes
-.TH highway 1 "Mon 29 Aug 2005"
+.TH highway 1 "Mon 22 Sep 2008"
.SH NAME
highway
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3highway\fP
.BI "-f" " highway.dat "
Generic data file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
-.TH make_edi 1 "Mon 29 Aug 2005"
+.TH make_edi 1 "Mon 22 Sep 2008"
.SH NAME
make_edi
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3make_edi\fP
.BI "-f" " eigenvec.trr "
.BI "-mon" " string "
.BI "-linfix" " string "
.BI "-linacc" " string "
+.BI "-flood" " string "
.BI "-radfix" " string "
.BI "-radacc" " string "
.BI "-radcon" " string "
-.BI "-flood" " string "
.BI "-outfrq" " int "
.BI "-slope" " real "
.BI "-maxedsteps" " int "
.BI "-accdir" " string "
.BI "-radstep" " real "
.BI "-[no]restrain" ""
-.BI "-[no]hesse" ""
+.BI "-[no]hessian" ""
.BI "-[no]harmonic" ""
.SH DESCRIPTION
.B make_edi
-generates an ED-sampling input file to be used with mdrun
+generates an essential dynamics (ED) sampling input file to be used with mdrun
based on eigenvectors of a covariance matrix (
.B g_covar
) or from a
-Normal Modes anaysis (
+normal modes anaysis (
.B g_nmeig
).
-ED-sampling can be used to manipulate the position along collective coordinates
+ED sampling can be used to manipulate the position along collective coordinates
(eigenvectors) of (biological) macromolecules during a simulation. Particularly,
it may be used to enhance the sampling efficiency of MD simulations by stimulating
the system to explore new regions along these collective coordinates. A number
to keep the position along a certain (set of) coordinate(s) fixed (
.B -linfix
),
-or to only monitor the projections of the positions, velocities and forces onto
-these coordinates(
+or to only monitor the projections of the positions onto
+these coordinates (
.B -mon
).
.B -mon
-: monitor projections of x, v and f onto selected eigenvectors.
+: monitor projections of the coordinates onto selected eigenvectors.
: perform acceptance radius contraction along selected eigenvectors
towards a target structure specified with
.B -tar
-.NOTE: each eigenvector can be selected only once.
+.
+
+NOTE: each eigenvector can be selected only once.
.B -outfrq
-: frequency (in steps) of writing out projections etc.
+: frequency (in steps) of writing out projections etc. to .edo file
+
.B -slope
before a new cycle is started.
Note on the parallel implementation: since ED sampling is a 'global' thing
-(collective coordinates etc), at least on the 'protein' side, ED sampling
-is not very parallel-friendly from an implentation point of view (it would
-require much extra communication to fully parallelize the algorithms).
-Fortunately, however, a typical parallel protein simulation in gromacs has
-most or all protein coordinates on one processor (the master) and has only
-other atoms (solvent, lipid, ions etc) on the other processors. With such a
-setup, ED sampling will still work. If the atoms over which ED sampling should
-be performed are spread over multiple processors, a fatal error will result.
-
-All output of mdrun (specify with -eo) is written to a .edo file (some extra
-information is written to the log file of mdrun too, actually). The .edo format
-is a simple ASCII file that should be easy to parse with standard unix tools
-like awk. A script (parse_edo) can be downloaded from contribution section at
- www.gromacs.org to extract information from the
-.edo files for your convinience. In short, the header defines which information
-can be expected in the rest of the .edo file. After the header, per step the
-following information is present:
+(collective coordinates etc.), at least on the 'protein' side, ED sampling
+is not very parallel-friendly from an implentation point of view. Because
+parallel ED requires much extra communication, expect the performance to be
+lower as in a free MD simulation, especially on a large number of nodes.
-* the step number
+All output of mdrun (specify with -eo) is written to a .edo file. In the output
+file, per OUTFRQ step the following information is present:
-* RMSD (for atoms in fitting prior to calculating ED constr.)
-* projections of the positions onto selected eigenvectors
-
-* projections of the velocities onto selected eigenvectors
+* the step number
-* projections of the forces onto selected eigenvectors
+* the number of the ED dataset. (Note that you can impose multiple ED constraints in
+a single simulation - on different molecules e.g. - if several .edi files were concatenated
+first. The constraints are applied in the order they appear in the .edi file.)
+* RMSD (for atoms involved in fitting prior to calculating the ED constraints)
+* projections of the positions onto selected eigenvectors
-All projections are in the same order as in the header, so if you have e.g.
-2 groups (say one group over which acceptance radius expansion is performed,
-and another for which the projections are merely monitored) then you first
-get the position projections for each of the 2 groups, then the velocities
-and then the forces. Radii are not explicitly written to the .edo file, as
-they can be readily projected back from the positions. Alternatively, radii
-may be 'grepped from the log file.
with -flood you can specify which eigenvectors are used to compute a flooding potential,
which will lead to extra forces expelling the structure out of the region described
-by the covariance matrix. if you switch -restrain the potential is inverted and the structure
-is kept in that region
+by the covariance matrix. If you switch -restrain the potential is inverted and the structure
+is kept in that region.
-the origin is normally the average structure stored in the eigvec.trr file
-it can be changed with -ori to an arbitrary position in configurational space
-with -tau , -deltaF0 and -Eflnull you control the flooding strength
-Efl is the flooding strength, it is updated according to the rule of adaptive flooding
-tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth)
-deltaF0 is the flooding strength you want to reach after tau ps of simulation
-to use constant Efl set -tau to zero
+The origin is normally the average structure stored in the eigvec.trr file.
+It can be changed with -ori to an arbitrary position in configurational space.
+With -tau, -deltaF0 and -Eflnull you control the flooding behaviour.
+Efl is the flooding strength, it is updated according to the rule of adaptive flooding.
+Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth).
+DeltaF0 is the flooding strength you want to reach after tau ps of simulation.
+To use constant Efl set -tau to zero.
-alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
-to give good results for most standard cases in flooding of proteins
-alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
-increase, this is mimicked by alpha1for restraining alpha1 can give you smaller width in the restraining potentialRESTART and FLOODING:
+to give good results for most standard cases in flooding of proteins.
+Alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
+increase, this is mimicked by alpha1.
+For restraining alpha1 can give you smaller width in the restraining potential.
+
+
+
+RESTART and FLOODING:
If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
-the output file and write them with your texteditor into the .edi file under DELTA_F0 and EFL_NULL
+the output file and manually put them into the .edi file under DELTA_F0 and EFL_NULL.
.SH FILES
.BI "-f" " eigenvec.trr"
.B Input
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-eig" " eigenval.xvg"
.B Input, Opt.
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-tar" " target.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-ori" " origin.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " sam.edi"
.B Output
ED sampling input
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-mon" " string" " "
- Indices of eigenvectors for projections of x, v and f (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
+ Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91
.BI "-linfix" " string" " "
Indices of eigenvectors for fixed increment linear sampling
.BI "-linacc" " string" " "
Indices of eigenvectors for acceptance linear sampling
+.BI "-flood" " string" " "
+ Indices of eigenvectors for flooding
+
.BI "-radfix" " string" " "
Indices of eigenvectors for fixed increment radius expansion
.BI "-radcon" " string" " "
Indices of eigenvectors for acceptance radius contraction
-.BI "-flood" " string" " "
- Indices of eigenvectors for flooding
-
.BI "-outfrq" " int" " 100"
- freqency (in steps) of writing output in .edo file
+ Freqency (in steps) of writing output in .edo file
-.BI "-slope" " real" " 0"
- minimal slope in acceptance radius expamsion
+.BI "-slope" " real" " 0 "
+ Minimal slope in acceptance radius expansion
.BI "-maxedsteps" " int" " 0"
- max nr of steps per cycle
+ Max nr of steps per cycle
-.BI "-deltaF0" " real" " 150"
- target destabilization energy - used for flooding
+.BI "-deltaF0" " real" " 150 "
+ Target destabilization energy - used for flooding
-.BI "-deltaF" " real" " 0"
- start deltaF with this parameter - default 0, i.g. nonzero values only needed for restart
+.BI "-deltaF" " real" " 0 "
+ Start deltaF with this parameter - default 0, i.e. nonzero values only needed for restart
-.BI "-tau" " real" " 0.1"
- coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength
+.BI "-tau" " real" " 0.1 "
+ Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength
.BI "-eqsteps" " int" " 0"
- number of steps to run without any perturbations
+ Number of steps to run without any perturbations
-.BI "-Eflnull" " real" " 0"
- this is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0.
+.BI "-Eflnull" " real" " 0 "
+ This is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0.
-.BI "-T" " real" " 300"
- T is temperature, the value is needed if you want to do flooding
+.BI "-T" " real" " 300 "
+ T is temperature, the value is needed if you want to do flooding
-.BI "-alpha" " real" " 1"
- scale width of gaussian flooding potential with alpha2
+.BI "-alpha" " real" " 1 "
+ Scale width of gaussian flooding potential with alpha2
.BI "-linstep" " string" " "
Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 -3.1")
.BI "-accdir" " string" " "
Directions for acceptance linear sampling - only sign counts! (put in quotes! "-1 +1 -1.1")
-.BI "-radstep" " real" " 0"
+.BI "-radstep" " real" " 0 "
Stepsize (nm/step) for fixed increment radius expansion
-.BI "-[no]restrain" " no"
- use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
+.BI "-[no]restrain" "no "
+ Use the flooding potential with inverted sign - effects as quasiharmonic restraining potential
-.BI "-[no]hesse" " no"
- the eigenvectors and eigenvalues are from a Hesse matrix
+.BI "-[no]hessian" "no "
+ The eigenvectors and eigenvalues are from a Hessian matrix
-.BI "-[no]harmonic" " no"
- the eigenvalues are interpreted as spring constant
+.BI "-[no]harmonic" "no "
+ The eigenvalues are interpreted as spring constant
-.TH make_ndx 1 "Mon 29 Aug 2005"
+.TH make_ndx 1 "Mon 22 Sep 2008"
.SH NAME
make_ndx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3make_ndx\fP
.BI "-f" " conf.gro "
.SH FILES
.BI "-f" " conf.gro"
.B Input, Opt.
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt., Mult.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
-.TH mdrun 1 "Mon 29 Aug 2005"
+.TH mdrun 1 "Mon 22 Sep 2008"
.SH NAME
mdrun
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3mdrun\fP
.BI "-s" " topol.tpr "
.BI "-o" " traj.trr "
.BI "-x" " traj.xtc "
+.BI "-cpi" " state.cpt "
+.BI "-cpo" " state.cpt "
.BI "-c" " confout.gro "
.BI "-e" " ener.edr "
.BI "-g" " md.log "
.BI "-field" " field.xvg "
.BI "-table" " table.xvg "
.BI "-tablep" " tablep.xvg "
+.BI "-tableb" " table.xvg "
.BI "-rerun" " rerun.xtc "
.BI "-tpi" " tpi.xvg "
+.BI "-tpid" " tpidist.xvg "
.BI "-ei" " sam.edi "
.BI "-eo" " sam.edo "
.BI "-j" " wham.gct "
.BI "-ffout" " gct.xvg "
.BI "-devout" " deviatie.xvg "
.BI "-runav" " runaver.xvg "
-.BI "-pi" " pull.ppa "
-.BI "-po" " pullout.ppa "
-.BI "-pd" " pull.pdo "
-.BI "-pn" " pull.ndx "
+.BI "-px" " pullx.xvg "
+.BI "-pf" " pullf.xvg "
.BI "-mtx" " nm.mtx "
.BI "-dn" " dipole.ndx "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-deffnm" " string "
.BI "-[no]xvgr" ""
-.BI "-np" " int "
-.BI "-nt" " int "
+.BI "-[no]pd" ""
+.BI "-dd" " vector "
+.BI "-npme" " int "
+.BI "-ddorder" " enum "
+.BI "-[no]ddcheck" ""
+.BI "-rdd" " real "
+.BI "-rcon" " real "
+.BI "-dlb" " enum "
+.BI "-dds" " real "
+.BI "-[no]sum" ""
.BI "-[no]v" ""
.BI "-[no]compact" ""
-.BI "-[no]sepdvdl" ""
-.BI "-[no]multi" ""
+.BI "-[no]seppot" ""
+.BI "-pforce" " real "
+.BI "-[no]reprod" ""
+.BI "-cpt" " real "
+.BI "-[no]append" ""
+.BI "-maxh" " real "
+.BI "-multi" " int "
.BI "-replex" " int "
.BI "-reseed" " int "
.BI "-[no]glas" ""
.SH DESCRIPTION
The mdrun program is the main computational chemistry engine
within GROMACS. Obviously, it performs Molecular Dynamics simulations,
-but it can also perform Brownian Dynamics and Langevin Dynamics
-as well as Conjugate Gradient or Steepest Descents energy minimization.
+but it can also perform Stochastic Dynamics, Energy Minimization,
+test particle insertion or (re)calculation of energies.
Normal mode analysis is another option. In this case mdrun
builds a Hessian matrix from single conformation.
For usual Normal Modes-like calculations, make sure that
-the structure provided is properly energy-minimised.
+the structure provided is properly energy-minimized.
The generated matrix can be diagonalized by g_nmeig.
+
The mdrun program reads the run input file (
.B -s
-) and distributes the
-topology over nodes if needed. The coordinates are passed
-around, so that computations can begin.
-First a neighborlist is made, then the forces are computed.
-The forces are globally summed, and the velocities and
-positions are updated. If necessary shake is performed to constrain
-bond lengths and/or bond angles.
-Temperature and Pressure can be controlled using weak coupling to a
-bath.
-
-
-mdrun produces at least three output file, plus one log file
-(
+)
+and distributes the topology over nodes if needed.
+mdrun produces at least four output files.
+A single log file (
.B -g
-) per node.
+) is written, unless the option
+
+.B -seppot
+is used, in which case each node writes a log file.
The trajectory file (
.B -o
), contains coordinates, velocities and
The energy file (
.B -e
) contains energies, the temperature,
-pressure, etc, a lot of these things are also printed in the log file
-of node 0.
+pressure, etc, a lot of these things are also printed in the log file.
Optionally coordinates can be written to a compressed trajectory file
(
.B -x
).
-When running in parallel with PVM or an old version of MPI the
-
-.B -np
-option must be given to indicate the number of
-nodes.
-
-
The option
.B -dgdl
is only used when free energy perturbation is
turned on.
+When mdrun is started using MPI with more than 1 node, parallelization
+is used. By default domain decomposition is used, unless the
+.B -pd
+
+option is set, which selects particle decomposition.
+
+
+With domain decomposition, the spatial decomposition can be set
+with option
+.B -dd
+. By default mdrun selects a good decomposition.
+The user only needs to change this when the system is very inhomogeneous.
+Dynamic load balancing is set with the option
+.B -dlb
+,
+which can give a significant performance improvement,
+especially for inhomogeneous systems. The only disadvantage of
+dynamic load balancing is that runs are no longer binary reproducible,
+but in most cases this is not important.
+By default the dynamic load balancing is automatically turned on
+when the measured performance loss due to load imbalance is 5% or more.
+At low parallelization these are the only important options
+for domain decomposition.
+At high parallelization the options in the next two sections
+could be important for increasing the performace.
+
+
+
+When PME is used with domain decomposition, separate nodes can
+be assigned to do only the PME mesh calculation;
+this is computationally more efficient starting at about 12 nodes.
+The number of PME nodes is set with option
+.B -npme
+,
+this can not be more than half of the nodes.
+By default mdrun makes a guess for the number of PME
+nodes when the number of nodes is larger than 11 or performance wise
+not compatible with the PME grid x dimension.
+But the user should optimize npme. Performance statistics on this issue
+are written at the end of the log file.
+For good load balancing at high parallelization,
+npme should be divisible by the number of PME nodes
+
+
+
+This section lists all options that affect the domain decomposition.
+
+
+Option
+.B -rdd
+can be used to set the required maximum distance
+for inter charge-group bonded interactions.
+Communication for two-body bonded interactions below the non-bonded
+cut-off distance always comes for free with the non-bonded communication.
+Atoms beyond the non-bonded cut-off are only communicated when they have
+missing bonded interactions; this means that the extra cost is minor
+and nearly indepedent of the value of
+.B -rdd
+.
+With dynamic load balancing option
+.B -rdd
+also sets
+the lower limit for the domain decomposition cell sizes.
+By default
+.B -rdd
+is determined by mdrun based on
+the initial coordinates. The chosen value will be a balance
+between interaction range and communication cost.
+
+
+When inter charge-group bonded interactions are beyond
+the bonded cut-off distance, mdrun terminates with an error message.
+For pair interactions and tabulated bonds
+that do not generate exclusions, this check can be turned off
+with the option
+.B -noddcheck
+.B .
+
+
+When constraints are present, option
+.B -rcon
+influences
+the cell size limit as well.
+Atoms connected by NC constraints, where NC is the LINCS order plus 1,
+should not be beyond the smallest cell size. A error message is
+generated when this happens and the user should change the decomposition
+or decrease the LINCS order and increase the number of LINCS iterations.
+By default mdrun estimates the minimum cell size required for P-LINCS
+in a conservative fashion. For high parallelization it can be useful
+to set the distance required for P-LINCS with the option
+.B -rcon
+.
+
+
+The
+.B -dds
+option sets the minimum allowed x, y and/or z scaling
+of the cells with dynamic load balancing. mdrun will ensure that
+the cells can scale down by at least this factor. This option is used
+for the automated spatial decomposition (when not using
+.B -dd
+)
+as well as for determining the number of grid pulses, which in turn
+sets the minimum allowed cell size. Under certain circumstances
+the value of
+.B -dds
+might need to be adjusted to account for
+high or low spatial inhomogeneity of the system.
+
+
+
+The option
+.B -nosum
+can be used to only sum the energies
+at every neighbor search step and energy output step.
+This can improve performance for highly parallel simulations
+where this global communication step becomes the bottleneck.
+For a global thermostat and/or barostat the temperature
+and/or pressure will also only be updated every nstlist steps.
+With this option the energy file will not contain averages and
+fluctuations over all integration steps.
+
+
With
.B -rerun
an input trajectory can be given for which
option is used to pass mdrun
a formatted table with potential functions. The file is read from
either the current directory or from the GMXLIB directory.
-A number of preformatted tables are presented in the GMXLIB dir,
+A number of pre-formatted tables are presented in the GMXLIB dir,
for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with
normal Coulomb.
-When pair interactions are present a seperate table for pair interaction
+When pair interactions are present a separate table for pair interaction
functions is read using the
.B -tablep
option.
+When tabulated bonded functions are present in the topology,
+interaction functions are read using the
+.B -tableb
+option.
+For each different tabulated interaction type the table file name is
+modified in a different way: before the file extension an underscore is
+appended, then a b for bonds, an a for angles or a d for dihedrals
+and finally the table number of the interaction type.
+
+
The options
.B -pi
,
With
.B -multi
multiple systems are simulated in parallel.
-As many (single node) input files are required as the number of nodes.
-The node number is appended to the run input and each output filename,
+As many input files are required as the number of systems.
+The system number is appended to the run input and each output filename,
for instance topol.tpr becomes topol0.tpr, topol1.tpr etc.
-The main use of this option is for NMR refinement: when distance
+The number of nodes per system is the total number of nodes
+divided by the number of systems.
+One use of this option is for NMR refinement: when distance
or orientation restraints are present these can be ensemble averaged
over all the systems.
With
.B -replex
replica exchange is attempted every given number
-of steps. This option implies
+of steps. The number of replicas is set with the
.B -multi
-, see above.
+option,
+see above.
All run input files should use a different coupling temperature,
the order of the files is not important. The random seed is set with
Finally some experimental algorithms can be tested when the
appropriate options have been given. Currently under
-investigation are: polarizibility, glass simulations
+investigation are: polarizability, glass simulations
and X-Ray bombardments.
+
+The option
+.B -pforce
+is useful when you suspect a simulation
+crashes due to too large forces. With this option coordinates and
+forces of atoms with a force larger than a certain value will
+be printed to stderr.
+
+
+
+Checkpoints containing the complete state of the system are written
+at regular intervals (option
+.B -cpt
+) to the file
+.B -cpo
+,
+unless option
+.B -cpt
+is set to -1.
+A simulation can be continued by reading the full state from file
+with option
+.B -cpi
+. This option is intelligent in the way that
+if no checkpoint file is found, Gromacs just assumes a normal run and
+starts from the first step of the tpr file.
+
+
+
+With checkpointing you can also use the option
+.B -append
+to
+just continue writing to the previous output files. This is not
+enabled by default since it is potentially dangerous if you move files,
+but if you just leave all your files in place and restart mdrun with
+exactly the same command (with options
+.B -cpi
+and
+.B -append
+)
+the result will be the same as from a single run. The contents will
+be binary identical (unless you use dynamic load balancing),
+but for technical reasons there might be some extra energy frames when
+using checkpointing (necessary for restarts without appending).
+
+
+
+With option
+.B -maxh
+a simulation is terminated and a checkpoint
+file is written at the first neighbor search step where the run time
+exceeds
+.B -maxh
+*0.99 hours.
+
+
+
When mdrun receives a TERM signal, it will set nsteps to the current
-step plus one. When mdrun receives a USR1 signal, it will set nsteps
-to the next multiple of nstxout after the current step.
+step plus one. When mdrun receives a USR1 signal, it will stop after
+the next neighbor search step (with nstlist=0 at the next step).
In both cases all the usual output will be written to file.
When running with MPI, a signal to one of the mdrun processes
is sufficient, this signal should not be sent to mpirun or
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-o" " traj.trr"
.B Output
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-x" " traj.xtc"
.B Output, Opt.
Compressed trajectory (portable xdr format)
+.BI "-cpi" " state.cpt"
+.B Input, Opt.
+ Checkpoint file
+
+.BI "-cpo" " state.cpt"
+.B Output, Opt.
+ Checkpoint file
+
.BI "-c" " confout.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-e" " ener.edr"
.B Output
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-g" " md.log"
.B Output
.B Input, Opt.
xvgr/xmgr file
+.BI "-tableb" " table.xvg"
+.B Input, Opt.
+ xvgr/xmgr file
+
.BI "-rerun" " rerun.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-tpi" " tpi.xvg"
.B Output, Opt.
xvgr/xmgr file
+.BI "-tpid" " tpidist.xvg"
+.B Output, Opt.
+ xvgr/xmgr file
+
.BI "-ei" " sam.edi"
.B Input, Opt.
ED sampling input
.B Output, Opt.
xvgr/xmgr file
-.BI "-pi" " pull.ppa"
-.B Input, Opt.
- Pull parameters
-
-.BI "-po" " pullout.ppa"
+.BI "-px" " pullx.xvg"
.B Output, Opt.
- Pull parameters
+ xvgr/xmgr file
-.BI "-pd" " pull.pdo"
+.BI "-pf" " pullf.xvg"
.B Output, Opt.
- Pull data output
-
-.BI "-pn" " pull.ndx"
-.B Input, Opt.
- Index file
+ xvgr/xmgr file
.BI "-mtx" " nm.mtx"
.B Output, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-deffnm" " string" " "
Set the default filename for all file options
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-np" " int" " 1"
- Number of nodes, must be the same as used for grompp
+.BI "-[no]pd" "no "
+ Use particle decompostion
-.BI "-nt" " int" " 1"
- Number of threads to start on each node
+.BI "-dd" " vector" " 0 0 0"
+ Domain decomposition grid, 0 is optimize
+
+.BI "-npme" " int" " -1"
+ Number of separate nodes to be used for PME, -1 is guess
+
+.BI "-ddorder" " enum" " interleave"
+ DD node order:
+.B interleave
+,
+.B pp_pme
+or
+.B cartesian
-.BI "-[no]v" " no"
+
+.BI "-[no]ddcheck" "yes "
+ Check for all bonded interactions with DD
+
+.BI "-rdd" " real" " 0 "
+ The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates
+
+.BI "-rcon" " real" " 0 "
+ Maximum distance for P-LINCS (nm), 0 is estimate
+
+.BI "-dlb" " enum" " auto"
+ Dynamic load balancing (with DD):
+.B auto
+,
+.B no
+or
+.B yes
+
+
+.BI "-dds" " real" " 0.8 "
+ Minimum allowed dlb scaling of the DD cell size
+
+.BI "-[no]sum" "yes "
+ Sum the energies at every step
+
+.BI "-[no]v" "no "
Be loud and noisy
-.BI "-[no]compact" " yes"
+.BI "-[no]compact" "yes "
Write a compact log file
-.BI "-[no]sepdvdl" " no"
+.BI "-[no]seppot" "no "
Write separate V and dVdl terms for each interaction type and node to the log file(s)
-.BI "-[no]multi" " no"
- Do multiple simulations in parallel (only with -np 1)
+.BI "-pforce" " real" " -1 "
+ Print all forces larger than this (kJ/mol nm)
+
+.BI "-[no]reprod" "no "
+ Try to avoid optimizations that affect binary reproducibility
+
+.BI "-cpt" " real" " 15 "
+ Checkpoint interval (minutes)
+
+.BI "-[no]append" "no "
+ Append to previous output files when restarting from checkpoint
+
+.BI "-maxh" " real" " -1 "
+ Terminate after 0.99 times this time (hours)
+
+.BI "-multi" " int" " 0"
+ Do multiple simulations in parallel
.BI "-replex" " int" " 0"
Attempt replica exchange every steps
.BI "-reseed" " int" " -1"
Seed for replica exchange, -1 is generate a seed
-.BI "-[no]glas" " no"
+.BI "-[no]glas" "no "
Do glass simulation with special long range corrections
-.BI "-[no]ionize" " no"
+.BI "-[no]ionize" "no "
Do a simulation including the effect of an X-Ray bombardment on your system
-.TH mk_angndx 1 "Mon 29 Aug 2005"
+.TH mk_angndx 1 "Mon 22 Sep 2008"
.SH NAME
mk_angndx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "-s" " topol.tpr "
.BI "-[no]h" ""
.BI "-nice" " int "
.BI "-type" " enum "
+.BI "-[no]hyd" ""
.SH DESCRIPTION
mk_angndx makes an index file for calculation of
angle distributions etc. It uses a run input file (
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " angle.ndx"
.B Output
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Type of angle:
.B angle
,
-.B g96-angle
-,
.B dihedral
,
.B improper
-,
-.B ryckaert-bellemans
or
-.B phi-psi
+.B ryckaert-bellemans
+
+.BI "-[no]hyd" "yes "
+ Include angles with atoms with mass 1.5
-.TH ngmx 1 "Mon 29 Aug 2005"
+.TH ngmx 1 "Mon 22 Sep 2008"
.SH NAME
ngmx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3ngmx\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
+.SH KNOWN PROBLEMS
\- Balls option does not work
\- Some times dumps core without a good reason
-.TH pdb2gmx 1 "Mon 29 Aug 2005"
+.TH pdb2gmx 1 "Mon 22 Sep 2008"
.SH NAME
pdb2gmx
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "-f" " eiwit.pdb "
.BI "-[no]ss" ""
.BI "-[no]ter" ""
.BI "-[no]lys" ""
+.BI "-[no]arg" ""
.BI "-[no]asp" ""
.BI "-[no]glu" ""
+.BI "-[no]gln" ""
.BI "-[no]his" ""
.BI "-angle" " real "
.BI "-dist" " real "
.SH FILES
.BI "-f" " eiwit.pdb"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " conf.gro"
.B Output
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.BI "-p" " topol.top"
.B Output
.BI "-q" " clean.pdb"
.B Output, Opt.
- Generic structure: gro g96 pdb xml
+ Structure file: gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]merge" " no"
+.BI "-[no]merge" "no "
Merge chains into one molecule definition
.BI "-ff" " string" " select"
.B f3c
-.BI "-[no]inter" " no"
- Set the next 6 options to interactive
+.BI "-[no]inter" "no "
+ Set the next 8 options to interactive
-.BI "-[no]ss" " no"
+.BI "-[no]ss" "no "
Interactive SS bridge selection
-.BI "-[no]ter" " no"
+.BI "-[no]ter" "no "
Interactive termini selection, iso charged
-.BI "-[no]lys" " no"
+.BI "-[no]lys" "no "
Interactive Lysine selection, iso charged
-.BI "-[no]asp" " no"
+.BI "-[no]arg" "no "
+ Interactive Arganine selection, iso charged
+
+.BI "-[no]asp" "no "
Interactive Aspartic Acid selection, iso charged
-.BI "-[no]glu" " no"
+.BI "-[no]glu" "no "
Interactive Glutamic Acid selection, iso charged
-.BI "-[no]his" " no"
+.BI "-[no]gln" "no "
+ Interactive Glutamine selection, iso neutral
+
+.BI "-[no]his" "no "
Interactive Histidine selection, iso checking H-bonds
-.BI "-angle" " real" " 135"
+.BI "-angle" " real" " 135 "
Minimum hydrogen-donor-acceptor angle for a H-bond (degrees)
-.BI "-dist" " real" " 0.3"
+.BI "-dist" " real" " 0.3 "
Maximum donor-acceptor distance for a H-bond (nm)
-.BI "-[no]una" " no"
+.BI "-[no]una" "no "
Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
-.BI "-[no]ignh" " no"
+.BI "-[no]ignh" "no "
Ignore hydrogen atoms that are in the pdb file
-.BI "-[no]missing" " no"
+.BI "-[no]missing" "no "
Continue when atoms are missing, dangerous
-.BI "-[no]v" " no"
+.BI "-[no]v" "no "
Be slightly more verbose in messages
-.BI "-posrefc" " real" " 1000"
+.BI "-posrefc" " real" " 1000 "
Force constant for position restraints
.BI "-vsite" " enum" " none"
.B aromatics
-.BI "-[no]heavyh" " no"
+.BI "-[no]heavyh" "no "
Make hydrogen atoms heavy
-.BI "-[no]deuterate" " no"
+.BI "-[no]deuterate" "no "
Change the mass of hydrogens to 2 amu
-.TH protonate 1 "Mon 29 Aug 2005"
+.TH protonate 1 "Mon 22 Sep 2008"
.SH NAME
protonate
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3protonate\fP
.BI "-s" " topol.tpr "
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-f" " traj.xtc"
.B Input, Opt.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " protonated.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
--- /dev/null
+.TH sigeps 1 "Mon 22 Sep 2008"
+.SH NAME
+sigeps
+.B VERSION 4.0_rc1
+.SH SYNOPSIS
+\f3sigeps\fP
+.BI "-o" " potje.xvg "
+.BI "-[no]h" ""
+.BI "-nice" " int "
+.BI "-[no]w" ""
+.BI "-[no]xvgr" ""
+.BI "-c6" " real "
+.BI "-cn" " real "
+.BI "-pow" " int "
+.BI "-sig" " real "
+.BI "-eps" " real "
+.BI "-A" " real "
+.BI "-B" " real "
+.BI "-C" " real "
+.BI "-qi" " real "
+.BI "-qj" " real "
+.BI "-sigfac" " real "
+.SH DESCRIPTION
+Sigeps is a simple utility that converts c6/c12 or c6/cn combinations
+to sigma and epsilon, or vice versa. It can also plot the potential
+in file. In addition it makes an approximation of a Buckingham potential
+to a Lennard Jones potential.
+.SH FILES
+.BI "-o" " potje.xvg"
+.B Output
+ xvgr/xmgr file
+
+.SH OTHER OPTIONS
+.BI "-[no]h" "no "
+ Print help info and quit
+
+.BI "-nice" " int" " 0"
+ Set the nicelevel
+
+.BI "-[no]w" "no "
+ View output xvg, xpm, eps and pdb files
+
+.BI "-[no]xvgr" "yes "
+ Add specific codes (legends etc.) in the output xvg files for the xmgrace program
+
+.BI "-c6" " real" " 0.001 "
+ c6
+
+.BI "-cn" " real" " 1e-06 "
+ constant for repulsion
+
+.BI "-pow" " int" " 12"
+ power of the repulsion term
+
+.BI "-sig" " real" " 0.3 "
+ sig
+
+.BI "-eps" " real" " 1 "
+ eps
+
+.BI "-A" " real" " 100000"
+ Buckingham A
+
+.BI "-B" " real" " 32 "
+ Buckingham B
+
+.BI "-C" " real" " 0.001 "
+ Buckingham C
+
+.BI "-qi" " real" " 0 "
+ qi
+
+.BI "-qj" " real" " 0 "
+ qj
+
+.BI "-sigfac" " real" " 0.7 "
+ Factor in front of sigma for starting the plot
+
-.TH tpbconv 1 "Mon 29 Aug 2005"
+.TH tpbconv 1 "Mon 22 Sep 2008"
.SH NAME
tpbconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3tpbconv\fP
.BI "-s" " topol.tpr "
.BI "-o" " tpxout.tpr "
.BI "-[no]h" ""
.BI "-nice" " int "
+.BI "-nsteps" " int "
+.BI "-runtime" " real "
.BI "-time" " real "
.BI "-extend" " real "
.BI "-until" " real "
.BI "-[no]zeroq" ""
-.BI "-[no]unconstrained" ""
+.BI "-[no]cont" ""
.SH DESCRIPTION
-tpbconv can edit run input files in three ways.
+tpbconv can edit run input files in four ways.
.B 1st.
-by creating a run input file
+by modifying the number of steps in a run input file
+with option
+.B -nsteps
+or option
+.B -runtime
+.
+
+
+
+.B 2st.
+(OBSOLETE) by creating a run input file
for a continuation run when your simulation has crashed due to e.g.
a full disk, or by making a continuation run input file.
-Note that a frame with coordinates and velocities is needed,
-which means that when you never write velocities, you can not use
-tpbconv and you have to start the run again from the beginning.
+This option is obsolete, since mdrun now writes and reads
+checkpoint files.
+Note that a frame with coordinates and velocities is needed.
When pressure and/or Nose-Hoover temperature coupling is used
an energy file can be supplied to get an exact continuation
of the original run.
-.B 2nd.
+.B 3nd.
by creating a tpx file for a subset of your original
tpx file, which is useful when you want to remove the solvent from
your tpx file, or when you want to make e.g. a pure Ca tpx file.
.B WARNING: this tpx file is not fully functional
.
-.B 3rd.
+.B 4rd.
by setting the charges of a specified group
to zero. This is useful when doing free energy estimates
-using the LIE (Linear Interactio Energy) method.
+using the LIE (Linear Interaction Energy) method.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.BI "-f" " traj.trr"
.B Input, Opt.
- Full precision trajectory: trr trj
+ Full precision trajectory: trr trj cpt
.BI "-e" " ener.edr"
.B Input, Opt.
- Generic energy: edr ene
+ Energy file: edr ene
.BI "-n" " index.ndx"
.B Input, Opt.
.BI "-o" " tpxout.tpr"
.B Output
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-time" " real" " -1"
+.BI "-nsteps" " int" " -1"
+ Change the number of steps
+
+.BI "-runtime" " real" " -1 "
+ Set the run time (ps)
+
+.BI "-time" " real" " -1 "
Continue from frame at this time (ps) instead of the last frame
-.BI "-extend" " real" " 0"
+.BI "-extend" " real" " 0 "
Extend runtime by this amount (ps)
-.BI "-until" " real" " 0"
+.BI "-until" " real" " 0 "
Extend runtime until this ending time (ps)
-.BI "-[no]zeroq" " no"
+.BI "-[no]zeroq" "no "
Set the charges of a group (from the index) to zero
-.BI "-[no]unconstrained" " yes"
- For a continuous trajectory, the constraints should not be solved before the first step (default)
+.BI "-[no]cont" "yes "
+ For exact continuation, the constraints should not be solved before the first step
-.TH trjcat 1 "Mon 29 Aug 2005"
+.TH trjcat 1 "Mon 22 Sep 2008"
.SH NAME
trjcat
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjcat\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " trajout.xtc"
.B Output, Mult.
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
-.BI "-b" " time" " -1"
+.BI "-b" " time" " -1 "
First time to use (ps)
-.BI "-e" " time" " -1"
+.BI "-e" " time" " -1 "
Last time to use (ps)
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only write frame when t MOD dt = first time (ps)
.BI "-prec" " int" " 3"
Precision for .xtc and .gro writing in number of decimal places
-.BI "-[no]vel" " yes"
+.BI "-[no]vel" "yes "
Read and write velocities if possible
-.BI "-[no]settime" " no"
+.BI "-[no]settime" "no "
Change starting time interactively
-.BI "-[no]sort" " yes"
+.BI "-[no]sort" "yes "
Sort trajectory files (not frames)
-.BI "-[no]keeplast" " no"
+.BI "-[no]keeplast" "no "
keep overlapping frames at end of trajectory
-.BI "-[no]cat" " no"
+.BI "-[no]cat" "no "
do not discard double time frames
-.TH trjconv 1 "Mon 29 Aug 2005"
+.TH trjconv 1 "Mon 22 Sep 2008"
.SH NAME
trjconv
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjconv\fP
.BI "-f" " traj.xtc "
.BI "-timestep" " time "
.BI "-pbc" " enum "
.BI "-ur" " enum "
-.BI "-center" " enum "
+.BI "-[no]center" ""
+.BI "-boxcenter" " enum "
.BI "-box" " vector "
+.BI "-trans" " vector "
.BI "-shift" " vector "
.BI "-fit" " enum "
.BI "-ndec" " int "
.BI "-[no]app" ""
.BI "-split" " time "
.BI "-[no]sep" ""
+.BI "-nzero" " int "
.BI "-[no]ter" ""
.BI "-dropunder" " real "
.BI "-dropover" " real "
select a subset of atoms
.B 3.
-remove periodicity from molecules
+change the periodicity representation
.B 4.
treatment:
*
-.B whole
-puts the atoms in the box and then makes
-broken molecules whole (a run input file is required).
-Atom number 1 of each molecule will be inside the box.
+.B mol
+puts the center of mass of molecules in the box.
*
-.B com
-puts the center of mass of all
-.I residues
-
-in the box. Not that this can break molecules that consist of
-more than one residue (e.g. proteins).
+.B res
+puts the center of mass of residues in the box.
*
-.B inbox
+.B atom
puts all the atoms in the box.
*
such that they are all closest to the center of mass of the cluster
which is iteratively updated. Note that this will only give meaningful
results if you in fact have a cluster. Luckily that can be checked
-afterwards using a trajectory viewer.
+afterwards using a trajectory viewer. Note also that if your molecules
+are broken this will not work either.
-
-.B -pbc
-is ignored when
-.B -fit
-or
-.B -pfit
-is set,
-in that case molecules will be made whole.
+*
+.B whole
+only makes broken molecules whole.
Option
.B -ur
sets the unit cell representation for options
-.B whole
+.B mol
+,
+.B res
and
-.B inbox
+.B atom
of
.B -pbc
.
is
.B tric
(see below), unless the option
-.B -center
+.B -boxcenter
is set differently.
.B -center
centers the system in the box. The user can
select the group which is used to determine the geometrical center.
-The center options are:
+Option
+.B -boxcenter
+sets the location of the center of the box
+for options
+.B -pbc
+and
+.B -center
+. The center options are:
.B tric
: half of the sum of the box vectors,
.B zero
: zero.
Use option
-.B -pbc whole
+.B -pbc mol
in addition to
.B -center
when you
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-o" " trajout.xtc"
.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-s" " topol.tpr"
.B Input, Opt.
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
.BI "-tu" " enum" " ps"
.B us
,
.B ms
-,
-.B s
-,
-.B m
or
-.B h
+.B s
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-skip" " int" " 1"
Only write every nr-th frame
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only write frame when t MOD dt = first time (ps)
-.BI "-dump" " time" " -1"
+.BI "-dump" " time" " -1 "
Dump frame nearest specified time (ps)
-.BI "-t0" " time" " 0"
+.BI "-t0" " time" " 0 "
Starting time (ps) (default: don't change)
-.BI "-timestep" " time" " 0"
+.BI "-timestep" " time" " 0 "
Change time step between input frames (ps)
.BI "-pbc" " enum" " none"
PBC treatment (see help text for full description):
.B none
,
-.B whole
+.B mol
+,
+.B res
,
-.B inbox
+.B atom
,
.B nojump
,
.B cluster
or
-.B com
+.B whole
.BI "-ur" " enum" " rect"
.B compact
-.BI "-center" " enum" " no"
- Center atoms in box:
-.B no
-,
+.BI "-[no]center" "no "
+ Center atoms in box
+
+.BI "-boxcenter" " enum" " tric"
+ Center for -pbc and -center:
.B tric
,
.B rect
.BI "-box" " vector" " 0 0 0"
Size for new cubic box (default: read from input)
+.BI "-trans" " vector" " 0 0 0"
+ All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact.
+
.BI "-shift" " vector" " 0 0 0"
All coordinates will be shifted by framenr*shift
,
.B rot+trans
,
+.B rotxy+transxy
+,
.B translation
or
.B progressive
.BI "-ndec" " int" " 3"
Precision for .xtc and .gro writing in number of decimal places
-.BI "-[no]vel" " yes"
+.BI "-[no]vel" "yes "
Read and write velocities if possible
-.BI "-[no]force" " no"
+.BI "-[no]force" "no "
Read and write forces if possible
-.BI "-trunc" " time" " -1"
+.BI "-trunc" " time" " -1 "
Truncate input trj file after this time (ps)
.BI "-exec" " string" " "
Execute command for every output frame with the frame number as argument
-.BI "-[no]app" " no"
+.BI "-[no]app" "no "
Append output
-.BI "-split" " time" " 0"
+.BI "-split" " time" " 0 "
Start writing new file when t MOD split = first time (ps)
-.BI "-[no]sep" " no"
+.BI "-[no]sep" "no "
Write each frame to a separate .gro, .g96 or .pdb file
-.BI "-[no]ter" " no"
+.BI "-nzero" " int" " 0"
+ Prepend file number in case you use the -sep flag with this number of zeroes
+
+.BI "-[no]ter" "no "
Use 'TER' in pdb file as end of frame in stead of default 'ENDMDL'
-.BI "-dropunder" " real" " 0"
+.BI "-dropunder" " real" " 0 "
Drop all frames below this value
-.BI "-dropover" " real" " 0"
+.BI "-dropover" " real" " 0 "
Drop all frames above this value
-.TH trjorder 1 "Mon 29 Aug 2005"
+.TH trjorder 1 "Mon 22 Sep 2008"
.SH NAME
trjorder
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3trjorder\fP
.BI "-f" " traj.xtc "
with any Gromacs program to analyze the n closest waters.
+
If the output file is a pdb file, the distance to the reference target
will be stored in the B-factor field in order to color with e.g. rasmol.
+
+
+
+With option
+.B -nshell
+the number of molecules within a shell
+of radius
+.B -r
+around the refernce group are printed.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Structure+mass(db): tpr tpb tpa gro g96 pdb xml
+ Structure+mass(db): tpr tpb tpa gro g96 pdb
.BI "-n" " index.ndx"
.B Input, Opt.
Index file
.BI "-o" " ordered.xtc"
-.B Output
- Generic trajectory: xtc trr trj gro g96 pdb
+.B Output, Opt.
+ Trajectory: xtc trr trj gro g96 pdb
.BI "-nshell" " nshell.xvg"
.B Output, Opt.
xvgr/xmgr file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
-.BI "-[no]xvgr" " yes"
+.BI "-[no]xvgr" "yes "
Add specific codes (legends etc.) in the output xvg files for the xmgrace program
.BI "-na" " int" " 3"
.BI "-da" " int" " 1"
Atom used for the distance calculation
-.BI "-[no]com" " no"
+.BI "-[no]com" "no "
Use the distance to the center of mass of the reference group
-.BI "-r" " real" " 0"
+.BI "-r" " real" " 0 "
Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
-.TH wheel 1 "Mon 29 Aug 2005"
+.TH wheel 1 "Mon 22 Sep 2008"
.SH NAME
wheel
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3wheel\fP
.BI "-f" " nnnice.dat "
Encapsulated PostScript (tm) file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 19"
.BI "-r0" " int" " 1"
The first residue number in the sequence
-.BI "-rot0" " real" " 0"
+.BI "-rot0" " real" " 0 "
Rotate around an angle initially (90 degrees makes sense)
.BI "-T" " string" " "
Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel)
-.BI "-[no]nn" " yes"
+.BI "-[no]nn" "yes "
Toggle numbers
-.TH x2top 1 "Mon 29 Aug 2005"
+.TH x2top 1 "Mon 22 Sep 2008"
.SH NAME
x2top
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3x2top\fP
.BI "-f" " conf.gro "
.BI "-r" " out.rtp "
.BI "-[no]h" ""
.BI "-nice" " int "
-.BI "-scale" " real "
.BI "-ff" " string "
+.BI "-[no]v" ""
.BI "-nexcl" " int "
.BI "-[no]H14" ""
.BI "-[no]alldih" ""
.BI "-[no]pairs" ""
.BI "-name" " string "
.BI "-[no]pbc" ""
+.BI "-[no]pdbq" ""
.BI "-[no]param" ""
.BI "-[no]round" ""
.BI "-kb" " real "
.SH FILES
.BI "-f" " conf.gro"
.B Input
- Generic structure: gro g96 pdb tpr tpb tpa xml
+ Structure file: gro g96 pdb tpr tpb tpa
.BI "-o" " out.top"
.B Output, Opt.
Residue Type file used by pdb2gmx
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-scale" " real" " 1.1"
- Scaling factor for bonds with unknown atom types relative to atom type O
+.BI "-ff" " string" " oplsaa"
+ Force field for your simulation. Type "select" for interactive selcection.
-.BI "-ff" " string" " select"
- Select the force field for your simulation.
+.BI "-[no]v" "no "
+ Generate verbose output in the top file.
.BI "-nexcl" " int" " 3"
Number of exclusions
-.BI "-[no]H14" " yes"
+.BI "-[no]H14" "yes "
Use 3rd neighbour interactions for hydrogen atoms
-.BI "-[no]alldih" " no"
+.BI "-[no]alldih" "no "
Generate all proper dihedrals
-.BI "-[no]remdih" " no"
+.BI "-[no]remdih" "no "
Remove dihedrals on the same bond as an improper
-.BI "-[no]pairs" " yes"
+.BI "-[no]pairs" "yes "
Output 1-4 interactions (pairs) in topology file
.BI "-name" " string" " ICE"
Name of your molecule
-.BI "-[no]pbc" " yes"
+.BI "-[no]pbc" "yes "
Use periodic boundary conditions.
-.BI "-[no]param" " no"
+.BI "-[no]pdbq" "no "
+ Use the B-factor supplied in a pdb file for the atomic charges
+
+.BI "-[no]param" "yes "
Print parameters in the output
-.BI "-[no]round" " yes"
+.BI "-[no]round" "yes "
Round off measured values
.BI "-kb" " real" " 400000"
Bonded force constant (kJ/mol/nm2)
-.BI "-kt" " real" " 400"
+.BI "-kt" " real" " 400 "
Angle force constant (kJ/mol/rad2)
-.BI "-kp" " real" " 5"
+.BI "-kp" " real" " 5 "
Dihedral angle force constant (kJ/mol/rad2)
+.SH KNOWN PROBLEMS
\- The atom type selection is primitive. Virtually no chemical knowledge is used
\- Periodic boundary conditions screw up the bonding
-.TH xpm2ps 1 "Mon 29 Aug 2005"
+.TH xpm2ps 1 "Mon 22 Sep 2008"
.SH NAME
xpm2ps
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "-f" " root.xpm "
.BI "-[no]yonce" ""
.BI "-legend" " enum "
.BI "-diag" " enum "
-.BI "-combine" " enum "
.BI "-size" " real "
.BI "-bx" " real "
.BI "-by" " real "
.BI "-skip" " int "
.BI "-[no]zeroline" ""
.BI "-legoffset" " int "
+.BI "-combine" " enum "
+.BI "-cmin" " real "
+.BI "-cmax" " real "
.SH DESCRIPTION
xpm2ps makes a beautiful color plot of an XPixelMap file.
Labels and axis can be displayed, when they are supplied
.B -diag
to
.B none
-. With
-
-.B -combine
-an alternative operation can be selected to combine
-the matrices. In this case, a new color map will be generated with
+.
+In this case, a new color map will be generated with
a red gradient for negative numbers and a blue for positive.
-
-
If the color coding and legend labels of both matrices are identical,
only one legend will be displayed, else two separate legends are
displayed.
+With
+.B -combine
+an alternative operation can be selected
+to combine the matrices. The output range is automatically set
+to the actual range of the combined matrix. This can be overridden
+with
+.B -cmin
+and
+.B -cmax
+.
X PixMap compatible matrix file
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-[no]w" " no"
+.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
-.BI "-[no]frame" " yes"
+.BI "-[no]frame" "yes "
Display frame, ticks, labels, title and legend
.BI "-title" " enum" " top"
.B none
-.BI "-[no]yonce" " no"
+.BI "-[no]yonce" "no "
Show y-label only once
.BI "-legend" " enum" " both"
.B none
-.BI "-combine" " enum" " halves"
- Combine two matrices:
-.B halves
-,
-.B add
-,
-.B sub
-,
-.B mult
-or
-.B div
-
-
-.BI "-size" " real" " 400"
+.BI "-size" " real" " 400 "
Horizontal size of the matrix in ps units
-.BI "-bx" " real" " 0"
+.BI "-bx" " real" " 0 "
Element x-size, overrides -size (also y-size when -by is not set)
-.BI "-by" " real" " 0"
+.BI "-by" " real" " 0 "
Element y-size
.BI "-rainbow" " enum" " no"
.BI "-skip" " int" " 1"
only write out every nr-th row and column
-.BI "-[no]zeroline" " no"
+.BI "-[no]zeroline" "no "
insert line in xpm matrix where axis label is zero
.BI "-legoffset" " int" " 0"
Skip first N colors from xpm file for the legend
+.BI "-combine" " enum" " halves"
+ Combine two matrices:
+.B halves
+,
+.B add
+,
+.B sub
+,
+.B mult
+or
+.B div
+
+
+.BI "-cmin" " real" " 0 "
+ Minimum for combination output
+
+.BI "-cmax" " real" " 0 "
+ Maximum for combination output
+
-.TH xrama 1 "Mon 29 Aug 2005"
+.TH xrama 1 "Mon 22 Sep 2008"
.SH NAME
xrama
-.B VERSION 3.3_beta_20050823
+.B VERSION 4.0_rc1
.SH SYNOPSIS
\f3xrama\fP
.BI "-f" " traj.xtc "
.SH FILES
.BI "-f" " traj.xtc"
.B Input
- Generic trajectory: xtc trr trj gro g96 pdb
+ Trajectory: xtc trr trj gro g96 pdb cpt
.BI "-s" " topol.tpr"
.B Input
- Generic run input: tpr tpb tpa xml
+ Run input file: tpr tpb tpa
.SH OTHER OPTIONS
-.BI "-[no]h" " no"
+.BI "-[no]h" "no "
Print help info and quit
.BI "-nice" " int" " 0"
Set the nicelevel
-.BI "-b" " time" " 0"
+.BI "-b" " time" " 0 "
First frame (ps) to read from trajectory
-.BI "-e" " time" " 0"
+.BI "-e" " time" " 0 "
Last frame (ps) to read from trajectory
-.BI "-dt" " time" " 0"
+.BI "-dt" " time" " 0 "
Only use frame when t MOD dt = first time (ps)
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>FAQ</h2><font size=-1><A HREF="online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 28 Aug 2005</B></td></tr></TABLE>
<HR>
<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
</div>
-</BODY>
\ No newline at end of file
+</BODY>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280>
<br><br>
<h2>
-GROMACS 4.0<br>
+GROMACS 3.3<br>
Online Reference</h2>
</td>
</TABLE></TD>
<td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 4.0<br>
+<B>VERSION 3.3<br>
Sun 28 Aug 2005</B></td>
</tr>
</table>
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</multicol>
<TR><TD><A HREF="online/genbox.html">genbox</A></TD><TD>solvates a system</TD>
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<TR><TD><A HREF="online/genconf.html">genconf</A></TD><TD>multiplies a conformation in 'random' orientations</TD>
-<TR><TD><A HREF="online/genpr.html">genpr</A></TD><TD>generates position restraints for index groups</TD>
+<TR><TD><A HREF="online/genrestr.html">genrestr</A></TD><TD>generates position restraints or distance restraints for index groups</TD>
<TR><TD><A HREF="online/protonate.html">protonate</A></TD><TD>protonates structures</TD>
</TABLE>
<TR><TD><A HREF="online/g_dist.html">g_dist</A></TD><TD>calculates the distances between the centers of mass of two groups</TD>
<TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates distances between atoms</TD>
<TR><TD><A HREF="online/g_mdmat.html">g_mdmat</A></TD><TD>calculates residue contact maps</TD>
+<TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
<TR><TD><A HREF="online/g_rmsdist.html">g_rmsdist</A></TD><TD>calculates atom pair distances averaged with power 2, -3 or -6</TD>
</TABLE>
<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
<TR><TD><A HREF="online/g_gyrate.html">g_gyrate</A></TD><TD>calculates the radius of gyration</TD>
<TR><TD><A HREF="online/g_msd.html">g_msd</A></TD><TD>calculates mean square displacements</TD>
+<TR><TD><A HREF="online/g_polystat.html">g_polystat</A></TD><TD>calculates static properties of polymers</TD>
<TR><TD><A HREF="online/g_rotacf.html">g_rotacf</A></TD><TD>calculates the rotational correlation function for molecules</TD>
-<TR><TD><A HREF="online/g_rdf.html">g_rdf</A></TD><TD>calculates radial distribution functions</TD>
+<TR><TD><A HREF="online/g_vanhove.html">g_vanhove</A></TD><TD>calculates Van Hove displacement functions</TD>
</TABLE>
<A NAME="HNR10">
<TR><TD><A HREF="online/g_saltbr.html">g_saltbr</A></TD><TD>computes salt bridges</TD>
<TR><TD><A HREF="online/g_sas.html">g_sas</A></TD><TD>computes solvent accessible surface area</TD>
<TR><TD><A HREF="online/g_order.html">g_order</A></TD><TD>computes the order parameter per atom for carbon tails</TD>
+<TR><TD><A HREF="online/g_principal.html">g_principal</A></TD><TD>calculates axes of inertia for a group of atoms</TD>
+<TR><TD><A HREF="online/g_rdf.html">g_rdf</A></TD><TD>calculates radial distribution functions</TD>
+<TR><TD><A HREF="online/g_sdf.html">g_sdf</A></TD><TD>calculates solvent distribution functions</TD>
<TR><TD><A HREF="online/g_sgangle.html">g_sgangle</A></TD><TD>computes the angle and distance between two groups</TD>
<TR><TD><A HREF="online/g_sorient.html">g_sorient</A></TD><TD>analyzes solvent orientation around solutes</TD>
+<TR><TD><A HREF="online/g_spol.html">g_spol</A></TD><TD>analyzes solvent dipole orientation and polarization around solutes</TD>
<TR><TD><A HREF="online/g_bundle.html">g_bundle</A></TD><TD>analyzes bundles of axes, e.g. helices</TD>
<TR><TD><A HREF="online/g_disre.html">g_disre</A></TD><TD>analyzes distance restraints</TD>
<TR><TD><A HREF="online/g_clustsize.html">g_clustsize</A></TD><TD>calculate size distributions of atomic clusters</TD>
<TR><TD><A HREF="online/g_traj.html">g_traj</A></TD><TD>plots x, v, f, box, temperature and rotational energy</TD>
<TR><TD><A HREF="online/g_velacc.html">g_velacc</A></TD><TD>calculates velocity autocorrelation functions</TD>
<TR><TD><A HREF="online/g_tcaf.html">g_tcaf</A></TD><TD>calculates viscosities of liquids</TD>
+<TR><TD><A HREF="online/g_kinetics.html">g_kinetics</A></TD><TD>derives information about kinetic processes from you trajectories</TD>
</TABLE>
<A NAME="HNR13">
<TR><TD><A HREF="online/g_potential.html">g_potential</A></TD><TD>calculates the electrostatic potential across the box</TD>
<TR><TD><A HREF="online/g_dipoles.html">g_dipoles</A></TD><TD>computes the total dipole plus fluctuations</TD>
<TR><TD><A HREF="online/g_dielectric.html">g_dielectric</A></TD><TD>calculates frequency dependent dielectric constants</TD>
+<TR><TD><A HREF="online/g_current.html">g_current</A></TD><TD>calculates dielectric constants for charged systems</TD>
</TABLE>
<A NAME="HNR14">
<TR><TD COLSPAN=2><b>Protein specific analysis</b>
<TR><TD><A HREF="online/do_dssp.html">do_dssp</A></TD><TD>assigns secondary structure and calculates solvent accessible surface area</TD>
<TR><TD><A HREF="online/g_chi.html">g_chi</A></TD><TD>calculates everything you want to know about chi and other dihedrals</TD>
-<TR><TD><A HREF="online/g_helix.html">g_helix</A></TD><TD>calculates everything you want to know about helices</TD>
+<TR><TD><A HREF="online/g_helix.html">g_helix</A></TD><TD>calculates basic properties of alpha helices</TD>
+<TR><TD><A HREF="online/g_helixorient.html">g_helixorient</A></TD><TD>calculates local pitch/bending/rotation/orientation inside helices</TD>
<TR><TD><A HREF="online/g_rama.html">g_rama</A></TD><TD>computes Ramachandran plots</TD>
<TR><TD><A HREF="online/xrama.html">xrama</A></TD><TD>shows animated Ramachandran plots</TD>
<TR><TD><A HREF="online/wheel.html">wheel</A></TD><TD>plots helical wheels</TD>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ssdump</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> ssdump.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-map</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="map.html"> ss.map</a></tt> </TD><TD> Input, Lib. </TD><TD> File that maps matrix data to colors </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sss</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>HEBT</tt> </TD><TD> Secondary structures for structure count </TD></TD>
</TABLE>
<P>
-<UL>
-<LI>The program is very slow
-</UL>
-<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>-angles</tt>. Both <tt>-box</tt> and <tt>-d</tt>
will center the system in the box.
<p>
-Option <tt>-bt</tt> determines the box type: <tt>tric</tt> is a
-triclinic box, <tt>cubic</tt> is a cubic box, <tt>dodecahedron</tt> is
-a rhombic dodecahedron and <tt>octahedron</tt> is a truncated octahedron.
+Option <tt>-bt</tt> determines the box type: <tt>triclinic</tt> is a
+triclinic box, <tt>cubic</tt> is a rectangular box with all sides equal
+<tt>dodecahedron</tt> represents a rhombic dodecahedron and <tt>octahedron</tt> is a truncated octahedron.
The last two are special cases of a triclinic box.
The length of the three box vectors of the truncated octahedron is the
shortest distance between two opposite hexagons.
<p>
Option <tt>-box</tt> requires only
one value for a cubic box, dodecahedron and a truncated octahedron.
-With <tt>-d</tt> and <tt>tric</tt> the size of the system in the x, y
+<p>
+With <tt>-d</tt> and a <tt>triclinic</tt> box the size of the system in the x, y
and z directions is used. With <tt>-d</tt> and <tt>cubic</tt>,
-<tt>dodecahedron</tt> or <tt>octahedron</tt> the diameter of the system
-is used, which is the largest distance between two atoms.
+<tt>dodecahedron</tt> or <tt>octahedron</tt> boxes, the dimensions are set
+to the diameter of the system (largest distance between atoms) plus twice
+the specified distance.
<p>
Option <tt>-angles</tt> is only meaningful with option <tt>-box</tt> and
a triclinic box and can not be used with option <tt>-d</tt>.
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mead</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pqr.html"> mead.pqr</a></tt> </TD><TD> Output, Opt. </TD><TD> Coordinate file for MEAD </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> bfact.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ndef</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Choose output from default index groups </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bt</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>tric</tt> </TD><TD> Box type for -box and -d: <tt>tric</tt>, <tt>cubic</tt>, <tt>dodecahedron</tt> or <tt>octahedron</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ndef</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Choose output from default index groups </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bt</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>triclinic</tt> </TD><TD> Box type for -box and -d: <tt>triclinic</tt>, <tt>cubic</tt>, <tt>dodecahedron</tt> or <tt>octahedron</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Box vector lengths (a,b,c) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-angles</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>90 90 90</tt> </TD><TD> Angles between the box vectors (bc,ac,ab) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Distance between the solute and the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]c</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Center molecule in box (implied by -box and -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Distance between the solute and the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]c</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center molecule in box (implied by -box and -d) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-center</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Coordinates of geometrical center </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-translate</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Translation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rotate</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Rotation around the X, Y and Z axes in degrees </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]princ</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Orient molecule(s) along their principal axes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]princ</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Orient molecule(s) along their principal axes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Scaling factor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-density</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1000</tt> </TD><TD> Density (g/l) of the output box achieved by scaling </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Compute and print volume of the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove the periodicity (make molecule whole again) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]grasp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rvdw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.12</tt> </TD><TD> Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sig56</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vdwread</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> Read the Van der Waals radii from the file vdwradii.<a href="dat.html">dat</a> rather than computing the radii based on the force field </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]atom</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Force B-factor attachment per atom </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]legend</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Make B-factor legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-density</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Density (g/l) of the output box achieved by scaling </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Compute and print volume of the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove the periodicity (make molecule whole again) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]grasp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Store the charge of the atom in the B-factor field and the radius of the atom in the occupancy field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rvdw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.12 </tt> </TD><TD> Default Van der Waals radius (in nm) if one can not be found in the database or if no parameters are present in the topology file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sig56</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Use rmin/2 (minimum in the Van der Waals potential) rather than sigma/2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vdwread</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> Read the Van der Waals radii from the file vdwradii.<a href="dat.html">dat</a> rather than computing the radii based on the force field </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]atom</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Force B-factor attachment per atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]legend</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make B-factor legend </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-label</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>A</tt> </TD><TD> Add chain label for all residues </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>For complex molecules, the periodicity removal routine may break down, in that case you can use <a href="trjconv.html">trjconv</a>
</UL>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Mult. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fixed.edr</a></tt> </TD><TD> Output </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Mult. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fixed.edr</a></tt> </TD><TD> Output </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to use </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to use </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write out frame when t MOD dt = offset </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-offset</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time offset for -dt option </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change starting time interactively </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sort energy files (not frames) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scalefac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Multiply energy component by this factor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]error</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Stop on errors in the file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to use </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write out frame when t MOD dt = offset </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-offset</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time offset for -dt option </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort energy files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scalefac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Multiply energy component by this factor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]error</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Stop on errors in the file </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>When combining trajectories the sigma and E^2 (necessary for statistics) are not updated correctly. Only the actual energy is correct. One thus has to compute statistics in another way.
</UL>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>File Formats</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<dl>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
</div>
-</BODY>
\ No newline at end of file
+</BODY>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>GROMACS<br>Flow chart</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<p>This is a flow chart of a typical GROMACS MD run of a protein
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
This is a simple ASCII format:<br>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
of a matrix. The numbers are proportional to the overlap of the square
root of the fluctuations. The normalized overlap is the most useful
number, it is 1 for identical matrices and 0 when the sampled
-subspaces are orthogonal.
+subspaces are orthogonal.<p>
+When the <tt>-entropy</tt> flag is given an entropy estimate will be
+computed based on the Quasiharmonic approach and based on
+Schlitter's formula.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec2.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec2.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eig</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eig2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval2.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-rmsf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> eigrmsf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-proj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> proj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-2d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> 2dproj.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> 3dproj.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-filt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">filtered.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-extr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> extreme.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> 3dproj.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-filt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">filtered.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-extr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> extreme.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-over</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> overlap.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-inpr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> inprod.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector for analysis (-1 is select) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>8</tt> </TD><TD> Last eigenvector for analysis (-1 is till the last) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyse every nr-th frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum for projection of the eigenvector on the average structure, max=0 gives the extremes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>2</tt> </TD><TD> Number of frames for the extremes output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split eigenvector projections where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]entropy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute entropy according to the Quasiharmonic formula or Schlitter's method. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for entropy calculations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nevskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>6</tt> </TD><TD> Number of eigenvalues to skip when computing the entropy due to the quasi harmonic approximation. When you do a rotational and/or translational fit prior to the covariance analysis, you get 3 or 6 eigenvalues that are very close to zero, and which should not be taken into account when computing the entropy. </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
standard deviation.<p>
Option <tt>-ac</tt> produces the autocorrelation function(s).<p>
Option <tt>-cc</tt> plots the resemblance of set i with a cosine of
-i/2 periods. The formula is:<br>2 (int0-T y(t) cos(pi t/i) dt)^2 / int0-T y(t) y(t) dt<br>
+i/2 periods. The formula is:<br>2 (int0-T y(t) cos(i pi t) dt)^2 / int0-T y(t) y(t) dt<br>
This is useful for principal components obtained from covariance
analysis, since the principal components of random diffusion are
pure cosines.<p>
to len/2. len is supplied with the option <tt>-filter</tt>.
This filter reduces oscillations with period len/2 and len by a factor
of 0.79 and 0.33 respectively.<p>
+Option <tt>-g</tt> fits the data to the function given with option
+<tt>-fitfn</tt>.<p>
Option <tt>-power</tt> fits the data to b t^a, which is accomplished
-by fitting to a t + b on log-log scale. All points after the first
-zero or negative value are ignored.
+by fitting to a t + b on <a href="log.html">log</a>-<a href="log.html">log</a> scale. All points after the first
+zero or negative value are ignored.<p>Option <tt>-luzar</tt> performs a Luzar & Chandler kinetics analysis
+on output from <tt><a href="g_hbond.html">g_hbond</a></tt>. The input file can be taken directly
+from <tt><a href="g_hbond.html">g_hbond</a> -ac</tt>, and then the same result should be produced.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Expect a time in the input </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to read from set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to read from set </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read # sets seperated by & </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the derivative </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Binwidth for the distribution </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Binwidth for the distribution </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-errbar</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Error bars for -av: <tt>none</tt>, <tt>stddev</tt>, <tt>error</tt> or <tt>90</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]integrate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Integrate data function(s) numerically using trapezium rule </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-aver_start</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Start averaging the integral from here </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xydy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interpret second data set as error in the y values for integrating </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-filter</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Print the high-frequency fluctuation after filtering with a cosine filter of length # </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]power</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Fit data to: b t^a </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]subav</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Subtract the average before autocorrelating </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]oneacf</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate one ACF over all sets </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]integrate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Integrate data function(s) numerically using trapezium rule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-aver_start</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start averaging the integral from here </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xydy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interpret second data set as error in the y values for integrating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]regression</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Perform a linear regression analysis on the data </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]luzar</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a Luzar and Chandler analysis on a correlation function and related as produced by <a href="g_hbond.html">g_hbond</a>. When in addition the -xydy flag is given the second and fourth column will be interpreted as errors in c(t) and n(t). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for the Luzar hydrogen bonding kinetics analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-filter</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Print the high-frequency fluctuation after filtering with a cosine filter of length # </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]power</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Fit data to: b t^a </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]subav</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Subtract the average before autocorrelating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]oneacf</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate one ACF over all sets </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> angle.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angdist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> angaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle to analyse: <tt>angle</tt>, <tt>dihedral</tt>, <tt>improper</tt> or <tt>ryckaert-bellemans</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> binwidth (degrees) for calculating the distribution </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot all angles separately in the averages file, in the order of appearance in the index file. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> binwidth (degrees) for calculating the distribution </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chandler</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use Chandler correlation function (N[trans] = 1, N[gauche] = 0) rather than cosine correlation function. Trans is defined as phi < -60 || phi > 60. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Average the correlation functions for the individual angles/dihedrals </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>Counting transitions only works for dihedrals with multiplicity 3
</UL>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bonds.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> bonds.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">distance.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-blen</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Bond length. By default length of first bond </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Half width of distribution as fraction of blen </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Average bond length distributions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]averdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Average distances (turns on -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-blen</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Bond length. By default length of first bond </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Half width of distribution as fraction of blen </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average bond length distributions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]averdist</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average distances (turns on -d) </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>It should be possible to get bond information from the topology.
</UL>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> bun_len.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">bun_dist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of axes </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the Z-axis as reference iso the average axis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the Z-axis as reference iso the average axis </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
With option <tt>-all</tt>, the angles themselves as a function of time for
each residue are printed to separate files (dihedral)(RESIDUE)(nresnr).<a href="xvg.html">xvg</a>.
These can be in radians or degrees.<p>
-A log file (argument <tt>-g</tt>) is also written. This contains <br>
+A <a href="log.html">log</a> file (argument <tt>-g</tt>) is also written. This contains <br>
(a) information about the number of residues of each type.<br>
(b) The NMR 3J coupling constants from the Karplus equation.<br>
(c) a table for each residue of the number of transitions between
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> order.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ss</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> ssdump.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> starting residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Phi dihedral angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]psi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Psi dihedral angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]omega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output for Omega dihedrals (peptide bonds) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rama</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Generate Phi/Psi and Chi1/Chi2 ramachandran plots </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]viol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write a file that gives 0 or 1 for violated Ramachandran angles </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output separate files for every dihedral. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rad</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> in angle vs time files, use radians rather than degrees. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]shift</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute chemical shifts from Phi/Psi angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Phi dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]psi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Psi dihedral angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]omega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output for Omega dihedrals (peptide bonds) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rama</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate Phi/Psi and Chi1/Chi2 ramachandran plots </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]viol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a file that gives 0 or 1 for violated Ramachandran angles </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]periodic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print dihedral angles modulo 360 degrees </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]all</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output separate files for every dihedral. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rad</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> in angle vs time files, use radians rather than degrees. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shift</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute chemical shifts from Phi/Psi angles </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-binwidth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> bin width for histograms (degrees) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-core_rotamer</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-core_rotamer</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> only the central -core_rotamer*(360/multiplicity) belongs to each rotamer (the rest is assigned to rotamer 0) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxchi</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> calculate first ndih Chi dihedrals: <tt>0</tt>, <tt>1</tt>, <tt>2</tt>, <tt>3</tt>, <tt>4</tt>, <tt>5</tt> or <tt>6</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normhisto</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize histograms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ramomega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> compute average omega as a function of phi/psi and plot it in an <a href="xpm.html">xpm</a> plot </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bfact</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>
-1</tt> </TD><TD> B-factor value for <a href="pdb.html">pdb</a> file for atoms with no calculated dihedral order parameter </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]chi_prod</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> compute a single cumulative rotamer for each residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]HChi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Include dihedrals to sidechain hydrogens </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax <= 0 means no limit. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normhisto</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize histograms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ramomega</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> compute average omega as a function of phi/psi and plot it in an <a href="xpm.html">xpm</a> plot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfact</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>
-1 </tt> </TD><TD> B-factor value for <a href="pdb.html">pdb</a> file for atoms with no calculated dihedral order parameter </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]chi_prod</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> compute a single cumulative rotamer for each residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]HChi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Include dihedrals to sidechain hydrogens </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum B-factor on any of the atoms that make up a dihedral, for the dihedral angle to be considere in the statistics. Applies to database work where a number of X-Ray structures is analyzed. -bmax <= 0 means no limit. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>Produces MANY output files (up to about 4 times the number of residues in the protein, twice that if autocorrelation functions are calculated). Typically several hundred files are output.
<LI>Phi and psi dihedrals are calculated in a non-standard way, using H-N-CA-C for phi instead of C(-)-N-CA-C, and N-CA-C-O for psi instead of N-CA-C-N(+). This causes (usually small) discrepancies with the output of other tools like <a href="g_rama.html">g_rama</a>.
<LI>-r0 option does not work properly
-<LI>Rotamers with multiplicity 2 are printed in chi.log as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
+<LI>Rotamers with multiplicity 2 are printed in chi.<a href="log.html">log</a> as if they had multiplicity 3, with the 3rd (g(+)) always having probability 0
</UL>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> rmsd.xpm</a></tt> </TD><TD> Input, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">rmsd-clust.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">clust-trans.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ntr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-trans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-clid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">clust-id.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">clusters.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">clusters.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dista</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use RMSD of distances instead of RMS deviation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize RMSD matrix in # levels </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyze every nr-th frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-wcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Write all structures for first # clusters to numbered files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nst</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write all structures if more than # per cluster </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rmsmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> minimum rms difference with rest of cluster for writing structures </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmsmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> minimum rms difference with rest of cluster for writing structures </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>linkage</tt> </TD><TD> Method for cluster determination: <tt>linkage</tt>, <tt>jarvis-patrick</tt>, <tt>monte-carlo</tt>, <tt>diagonalization</tt> or <tt>gromos</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-minstruct</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Minimum number of structures in cluster for coloring in the <a href="xpm.html">xpm</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]binary</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-M</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of nearest neighbors considered for Jarvis-Patrick algorithm, 0 is use cutoff </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of identical nearest neighbors required to form a cluster </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Random number seed for Monte Carlo clustering algorithm </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-niter</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10000</tt> </TD><TD> Number of iterations for MC </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-kT</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.001</tt> </TD><TD> Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kT</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Boltzmann weighting factor for Monte Carlo optimization (zero turns off uphill steps) </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fit.pdb</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> fit.pdb</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> fit1.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> fit2.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> match.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only write the fitted structure to file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Mass-weighted fitting and RMSD </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Try to make molecules whole again </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Do least squares superposition of the target structure to the reference </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]name</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only compare matching atom names </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bfac</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Output B-factors from atomic MSD values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only write the fitted structure to file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass-weighted fitting and RMSD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to make molecules whole again </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do least squares superposition of the target structure to the reference </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]name</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only compare matching atom names </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]label</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Added chain labels A for first and B for second structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bfac</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Output B-factors from atomic MSD values </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> average.pdb</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> average.pdb</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> covar.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ascii</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> covar.dat</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-xpm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> covar.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Fit to a reference structure </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Fit to a reference structure </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ref</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the deviation from the conformation in the structure file instead of from the average </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mwa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Mass-weighted covariance analysis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Last eigenvector to write away (-1 is till the last) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Apply corrections for periodic boundary conditions </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">electrons.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> density.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]number</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate number density instead of mass density. Hydrogens are not counted! </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ed</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate electron density instead of mass density </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]count</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only count atoms in slices, no densities. Hydrogens are not counted </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of groups to compute densities of </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]symm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Symmetrize the density along the axis, with respect to the center. Useful for bilayers. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dens</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>mass</tt> </TD><TD> Density: <tt>mass</tt>, <tt>number</tt>, <tt>charge</tt> or <tt>electron</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to compute densities of </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]symm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Symmetrize the density along the axis, with respect to the center. Useful for bilayers. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Shift the center of mass along the axis to zero. This means if your axis is Z and your box is bX, bY, bZ, the center of mass will be at bX/2, bY/2, 0. </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>When calculating electron densities, atomnames are used instead of types. This is bad.
-<LI>When calculating number densities, atoms with names that start with H are not counted. This may be surprising if you use hydrogens with names like OP3.
</UL>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_densmap</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
The output <tt>.<a href="xpm.html">xpm</a></tt> file can be visualized with for instance xv
and can be converted to postscript with <a href="xpm2ps.html">xpm2ps</a>.
<p>
-The default analysis is a 2-D number-density map for a selected
-group of atoms in the x-z plane. The grid spacing is set with the option
-<tt>-bin</tt>. When <tt>-nx</tt> or <tt>-nz</tt> is non-zero, the grid
-size is set by this option. Box size fluctuations are properly taken
-into account.
+The default analysis is a 2-D number-density <a href="map.html">map</a> for a selected
+group of atoms in the x-y plane.
+The averaging direction can be changed with the option <tt>-aver</tt>.
+When <tt>-xmin</tt> and/or <tt>-xmax</tt> are set only atoms that are
+within the limit(s) in the averaging direction are taken into account.
+The grid spacing is set with the option <tt>-bin</tt>.
+When <tt>-n1</tt> or <tt>-n2</tt> is non-zero, the grid
+size is set by this option.
+Box size fluctuations are properly taken into account.
<p>
When options <tt>-amax</tt> and <tt>-rmax</tt> are set, an axial-radial
-number-density map is made. Three groups should be supplied, the centers
+number-density <a href="map.html">map</a> is made. Three groups should be supplied, the centers
of mass of the first two groups define the axis, the third defines the
analysis group. The axial direction goes from -amax to +amax, where
the center is defined as the midpoint between the centers of mass and
The radial direction goes from 0 to rmax or from -rmax to +rmax
when the <tt>-mirror</tt> option has been set.
<p>
+The normalization of the output is set with the <tt>-unit</tt> option.
+The default produces a true number density. Unit <tt>nm-2</tt> leaves out
+the normalization for the averaging or the angular direction.
+Option <tt>count</tt> produces the count for each grid cell.
When you do not want the scale in the output to go
from zero to the maximum density, you can set the maximum
with the option <tt>-dmax</tt>.
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> densmap.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.02</tt> </TD><TD> Grid size </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nx</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in x direction </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in z direction </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-amax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum axial distance from the center </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum radial distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mirror</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Add the mirror image below the axial axis </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum density (0 means calculate it) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Grid size (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-aver</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> The direction to average over: <tt>z</tt>, <tt>y</tt> or <tt>x</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum coordinate for averaging </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-xmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum coordinate for averaging </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n1</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in the first direction </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-n2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of grid cells in the second direction </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-amax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum axial distance from the center </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum radial distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mirror</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Add the mirror image below the axial axis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-unit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>nm-3</tt> </TD><TD> Unit for the output: <tt>nm-3</tt>, <tt>nm-2</tt> or <tt>count</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum density in output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum density in output (0 means calculate it) </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> Mtot.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dipcorr.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> deriv.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> epsw.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> cole.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> use first column as X axis rather than first data set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Time were to end the integration of the data and start to use the fit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Begin time of fit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 500</tt> </TD><TD> End time of fit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 500</tt> </TD><TD> Length of function including data and tail from fit </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> Start value for fit parameter A </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 10</tt> </TD><TD> Start value for fit parameter tau1 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Start value for fit parameter tau2 </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 80</tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 78.5</tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fft</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> use fast fourier transform for correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x1</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> use first column as X axis rather than first data set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eint</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Time were to end the integration of the data and start to use the fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Begin time of fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-efit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500 </tt> </TD><TD> End time of fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>500 </tt> </TD><TD> Length of function including data and tail from fit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-A</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Start value for fit parameter A </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau1</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Start value for fit parameter tau1 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Start value for fit parameter tau2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>80 </tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>78.5 </tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nsmooth</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of points for smoothing </TD></TD>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html"> hello.out</a></tt> </TD><TD> Output </TD><TD> Generic output file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Perform cluster analysis in dihedral space instead of analysing dihedral transitions. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sa</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Perform cluster analysis in dihedral space instead of analysing dihedral transitions. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-mult</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> mulitiplicity for dihedral angles (by default read from topology) </TD></TD>
</TABLE>
<P>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_dipoles computes the total dipole plus fluctuations of a simulation
system. From this you can compute e.g. the dielectric constant for
-low dielectric media<p>
+low dielectric media.
+For molecules with a net charge, the net charge is subtracted at
+center of mass of the molecule.<p>
The file Mtot.<a href="xvg.html">xvg</a> contains the total dipole moment of a frame, the
components as well as the norm of the vector.
The file aver.<a href="xvg.html">xvg</a> contains < |Mu|^2 > and < |Mu| >^2 during the
The file dipdist.<a href="xvg.html">xvg</a> contains the distribution of dipole moments during
the simulation
The mu_max is used as the highest value in the distribution graph.<p>
-Furthermore the dipole autocorrelation function will be computed, when
-option -c is used. It can be averaged over all molecules,
-or (with option -avercorr) it can be computed as the autocorrelation
-of the total dipole moment of the simulation box.<p>
-At the moment the dielectric constant is calculated only correct if
-a rectangular or cubic simulation box is used.<p>
+Furthermore the dipole autocorrelation function will be computed when
+option -corr is used. The output file name is given with the <tt>-c</tt>
+option.
+The correlation functions can be averaged over all molecules
+(<tt>mol</tt>), plotted per molecule seperately (<tt>molsep</tt>)
+or it can be computed over the total dipole moment of the simulation box
+(<tt>total</tt>).<p>
Option <tt>-g</tt> produces a plot of the distance dependent Kirkwood
G-factor, as well as the average cosine of the angle between the dipoles
as a function of the distance. The plot also includes gOO and hOO
the dipoles divided by the distance to the third power.<p>
<p>
EXAMPLES<p>
-g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
--nofft<p>
+g_dipoles -corr mol -P1 -o dip_sqr -mu 2.273 -mumax 5.0 -nofft<p>
This will calculate the autocorrelation function of the molecular
dipoles using a first order Legendre polynomial of the angle of the
dipole vector and itself a time t later. For this calculation 1001
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-enx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-enx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> Mtot.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eps</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> epsilon.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-adip</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> adip.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dip3d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dip3d.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-cos</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> cosaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cmap</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> cmap.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">quadrupole.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-slab</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> slab.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-mu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> dipole of a single molecule (in Debye) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> max dipole in Debye (for histrogram) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mu</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> dipole of a single molecule (in Debye) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mumax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> max dipole in Debye (for histrogram) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-epsilonRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> epsilon of the reaction field used during the simulation, needed for dieclectric constant calculation. WARNING: 0.0 means infinity (default) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip steps in the output (but not in the computations) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> average temperature of the simulation (needed for dielectric constant calculation) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]avercorr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> calculate AC function of average dipole moment of the simulation box rather than average of AC function per molecule </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Calculate |cos theta| between all pairs of molecules. May be slow </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Average temperature of the simulation (needed for dielectric constant calculation) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Correlation function to calculate: <tt>none</tt>, <tt>mol</tt>, <tt>molsep</tt> or <tt>total</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Calculate |cos theta| between all pairs of molecules. May be slow </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ncos</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Must be 1 or 2. Determines whether the <cos> is computed between all mole cules in one group, or between molecules in two different groups. This turns on the -gkr flag. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-axis</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the computational box in direction X, Y or Z. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Divide the box in #nr slices. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gkratom</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Use the n-th atom of a molecule (starting from 1) to calculate the distance between molecules rather than the center of charge (when 0) in the calculation of distance dependent Kirkwood factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-gkratom2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Same as previous option in case ncos = 2, i.e. dipole interaction between two groups of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rcmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance to use in the dipole orientation distribution (with ncos == 2). If zero, a criterium based on the box length will be used. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]phi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot the 'torsion angle' defined as the rotation of the two dipole vectors around the distance vector between the two molecules in the <a href="xpm.html">xpm</a> file from the -cmap option. By default the cosine of the angle between the dipoles is plotted. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of colors in the cmap output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ndegrees</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>90</tt> </TD><TD> Number of divisions on the y-axis in the camp output (for 180 degrees) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_disre computes violations of distance restraints.
If necessary all protons can be added to a protein molecule
using the <a href="protonate.html">protonate</a> program.<p>
-The program allways
+The program always
computes the instantaneous violations rather than time-averaged,
because this analysis is done from a trajectory file afterwards
it does not make sense to use time averaging. However,
-the time averaged values per restraint are given in the
log file.<p>
+the time averaged values per restraint are given in the
<a href="log.html">log</a> file.<p>
An index file may be used to select specific restraints for
printing.<p>
When the optional<tt>-q</tt> flag is given a <a href="pdb.html">pdb</a> file coloured by the
When the <tt>-c</tt> option is given, an index file will be read
containing the frames in your trajectory corresponding to the clusters
(defined in another manner) that you want to analyze. For these clusters
-the program will compute average violations using the thisd power
-averaging algorithm and print them in the log file.
+the program will compute average violations using the third power
+averaging algorithm and print them in the <a href="log.html">log</a> file.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ds</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> drsum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> draver.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> drnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> viol.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> viol.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> clust.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> matrix.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of large violations that are stored in the log file every step </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of large violations that are stored in the <a href="log.html">log</a> file every step </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxdr</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance violation in matrix output. If less than or equal to 0 the maximum will be determined by the data. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of levels in the matrix output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]third</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use inverse third power averaging or linear for matrix output </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
x, y and z components are plotted.<p>
Or when <tt>-dist</tt> is set, print all the atoms in group 2 that are
closer than a certain distance to the center of mass of group 1.<p>
+With options <tt>-lt</tt> and <tt>-dist</tt> the number of contacts
+of all atoms in group 2 that are closer than a certain distance
+to the center of mass of group 1 are plotted as a function of the time
+that the contact was continously present.<p>
Other programs that calculate distances are <tt><a href="g_mindist.html">g_mindist</a></tt>
and <tt><a href="g_bond.html">g_bond</a></tt>.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-lt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">lifetime.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Print all atoms in group 2 closer than dist to the center of mass of group 1 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Print all atoms in group 2 closer than dist to the center of mass of group 1 </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_dyndom reads a <a href="pdb.html">pdb</a> file output from DynDom
-http://md.chem.rug.nl/~steve/DynDom/dyndom.home.html
+http://www.cmp.uea.ac.uk/dyndom/
It reads the coordinates, and the coordinates of the rotation axis
furthermore it reads an index file containing the domains.
Furthermore it takes the first and last atom of the arrow file
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> dyndom.pdb</a></tt> </TD><TD> Input </TD><TD> Protein data bank file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rotated.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rotated.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> domains.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-firstangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-lastangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-firstangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-lastangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Angle of rotation about rotation vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframe</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of steps on the pathway </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> DymDom dtermined angle of rotation about rotation vector </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Translation (Aangstroem) along rotation vector (see DynDom info file) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxangle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> DymDom dtermined angle of rotation about rotation vector </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translation (Aangstroem) along rotation vector (see DynDom info file) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-head</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> First atom of the arrow vector </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tail</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Last atom of the arrow vector </TD></TD>
</TABLE>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Finally, the total interaction energy energy per group can be
calculated (<tt>-etot</tt>).<p>
An approximation of the free energy can be calculated using:
-E(free) = E0 + kT log( <exp((E-E0)/kT)> ), where '<>'
+E(free) = E0 + kT <a href="log.html">log</a>( <exp((E-E0)/kT)> ), where '<>'
stands for time-average. A file with reference free energies
can be supplied to calculate the free energy difference
with some reference state. Group names (e.g. residue names)
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-groups</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> groups.dat</a></tt> </TD><TD> Input </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eref</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> eref.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-emat</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> emat.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mean</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> with -groups extracts matrix of mean energies in stead of matrix for each timestep </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mean</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> with -groups extracts matrix of mean energies in stead of matrix for each timestep </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> number of levels for matrix colors </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1e+20</tt> </TD><TD> max value for energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1e+20 </tt> </TD><TD> max value for energies </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1e+20</tt> </TD><TD> min value for energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> extract Coulomb SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coulr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Coulomb LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Coulomb 1-4 energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> extract Lennard-Jones SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Lennard-Jones LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Lennard-Jones 1-4 energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamsr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Buckingham SR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamlr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> extract Buckingham LR energies </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> calculate free energy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> reference temperature for free energy calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Coulomb SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coulr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]coul14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Coulomb 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> extract Lennard-Jones SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lj14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Lennard-Jones 1-4 energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamsr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham SR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]bhamlr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> extract Buckingham LR energies </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]free</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> calculate free energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> reference temperature for free energy calculation </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Average and RMSD are calculated with full precision from the
simulation (see printed manual). Drift is calculated by performing
a LSQ fit of the data to a straight line. Total drift is drift
-multiplied by total time.<p>
+multiplied by total time. The term fluctuation gives the RMSD around
+the LSQ fit.<p>
When the <tt>-viol</tt> option is set, the time averaged
violations are plotted and the running time-averaged and
instantaneous sum of violations are recalculated. Additionally
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> energy.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-viol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">violaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-pairs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pairs.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do a free energy estimate </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fetemp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> Reference temperature for free energy calculation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-zero</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Subtract a zero-point energy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print energies in high precision </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fee</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a free energy estimate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fetemp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Reference temperature for free energy calculation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-zero</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Subtract a zero-point energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sum the energy terms selected rather than display them all </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]dp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print energies in high precision </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mutot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute the total dipole moment from the components </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]uni</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Skip non-uniformly spaced frames </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip number of frames between data points </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print also the X1,t and sigma1,t, only if only 1 energy is requested </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print also the X1,t and sigma1,t, only if only 1 energy is requested </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of molecules in your sample: the energies are divided by this number </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of degrees of freedom per molecule. Necessary for calculating the heat capacity </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Also plot the eigenvectors with -oten </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ovec</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also plot the eigenvectors with -oten </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_gyrate computes the radius of gyration of a group of atoms
and the radii of gyration about the x, y and z axes,
-as a function of time. The atoms are explicitly mass weighted.
+as a function of time. The atoms are explicitly mass weighted.<p>
With the <tt>-nmol</tt> option the radius of gyration will be calculated
for multiple molecules by splitting the analysis group in equally
-sized parts.
+sized parts.<p>
+With the option <tt>-nz</tt> 2D radii of gyration in the x-y plane
+of slices along the z-axis are calculated.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gyrate.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-acf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> moi-acf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The number of molecules to analyze </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use absolute value of the charge of an atom as weighting factor instead of mass </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]p</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate the radii of gyration about the principal axes. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]moi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate the moments of inertia (defined by the principal axes). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use absolute value of the charge of an atom as weighting factor instead of mass </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]p</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the radii of gyration about the principal axes. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]moi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the moments of inertia (defined by the principal axes). </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nz</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate the 2D radii of gyration of # slices along the z-axis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-nm</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>The program assigns whole water molecules to a slice, based on the firstatom of three in the index file group. It assumes an order O,H,H.Name is not important, but the order is. If this demand is not met,assigning molecules to slices is different.
</UL>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_hbond computes and analyzes hydrogen bonds. Hydrogen bonds are
-determined based on cutoffs for the angle Donor - Hydrogen - Acceptor
+determined based on cutoffs for the angle Acceptor - Donor - Hydrogen
(zero is extended) and the distance Hydrogen - Acceptor.
OH and NH groups are regarded as donors, O is an acceptor always,
N is an acceptor by default, but this can be switched using
If you set -shell, you will be asked for an additional index group
which should contain exactly one atom. In this case, only hydrogen
bonds between atoms within the shell distance from the one atom are
-considered.<p>It is also possible to analyse specific hydrogen bonds with
-<tt>-sel</tt>. This index file must contain a group of atom triplets
-Donor Hydrogen Acceptor, in the following way:<p>
-<tt>
+considered.<p><tt>
[ selected ]<br>
20 21 24<br>
25 26 29<br>
into hydrogen bonds. Ordering is identical to that in <tt>-hbn</tt>
index file.<br>
<tt>-dan</tt>: write out the number of donors and acceptors analyzed for
-each timeframe. This is especially usefull when using <tt>-shell</tt>.
+each timeframe. This is especially usefull when using <tt>-shell</tt>.<br>
+<tt>-nhbdist</tt>: compute the number of HBonds per hydrogen in order to
+compare results to Raman Spectroscopy.
<p>
Note: options <tt>-ac</tt>, <tt>-life</tt>, <tt>-hbn</tt> and <tt>-hbm</tt>
require an amount of memory proportional to the total numbers of donors
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> hbond.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-sel</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> select.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-num</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbnum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> hbond.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ac</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbac.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbdist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ang</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hbang.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-don</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> donor.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dan</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> danum.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-life</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> hblife.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-nhbdist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> nhbdist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ins</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Analyze solvent insertion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 30</tt> </TD><TD> Cutoff angle (degrees, Donor - Hydrogen - Acceptor) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.35</tt> </TD><TD> Cutoff radius (nm, X - Acceptor, see next option) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]da</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-abin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Binwidth angle distribution (degrees) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.005</tt> </TD><TD> Binwidth distance distribution (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]contact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do not look for hydrogen bonds, but merely for contacts within the cut-off distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> when > 0, only calculate hydrogen bonds within # nm shell around one particle </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Time from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ins</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Analyze solvent insertion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-a</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>30 </tt> </TD><TD> Cutoff angle (degrees, Acceptor - Donor - Hydrogen) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.35 </tt> </TD><TD> Cutoff radius (nm, X - Acceptor, see next option) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]da</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use distance Donor-Acceptor (if TRUE) or Hydrogen-Acceptor (FALSE) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r2</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Second cutoff radius. Mainly useful with -contact and -ac </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-abin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Binwidth angle distribution (degrees) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.005 </tt> </TD><TD> Binwidth distance distribution (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nitacc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Regard nitrogen atoms as acceptors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]contact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do not look for hydrogen bonds, but merely for contacts within the cut-off distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> when > 0, only calculate hydrogen bonds within # nm shell around one particle </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fitstart</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Time (ps) from which to start fitting the correlation functions in order to obtain the forward and backward rate constants for HB breaking and formation </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature (K) for computing the Gibbs energy corresponding to HB breaking and reforming </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-smooth</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> If >= 0, the tail of the ACF will be smoothed by fitting it to an exponential function: y = A exp(-x/tau) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Dump the first N hydrogen bond ACFs in a single <a href="xvg.html">xvg</a> file for debugging </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max_hb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max_hb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Theoretical maximum number of hydrogen bonds used for normalizing HB autocorrelation function. Can be useful in case the program estimates it wrongly </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> H-bonds between the same donor and acceptor, but with different hydrogen are treated as a single H-bond. Mainly important for the ACF. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
+<UL>
+<LI>The option <tt>-sel</tt> that used to work on selected hbonds is out of order, and therefore not available for the time being.
+</UL>
+<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-to</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="g87.html"> gtraj.g87</a></tt> </TD><TD> Output, Opt. </TD><TD> Gromos-87 ASCII trajectory format </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> zconf.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> waver.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cz</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> zconf.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> waver.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Check at every step which part of the sequence is helical </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]F</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Toggle fit to a perfect helix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]db</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print debug info </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]q</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check at every step which part of the sequence is helical </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]F</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle fit to a perfect helix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]db</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print debug info </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-prop</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>RAD</tt> </TD><TD> Select property to weight eigenvectors with. WARNING experimental stuff: <tt>RAD</tt>, <tt>TWIST</tt>, <tt>RISE</tt>, <tt>LEN</tt>, <tt>NHX</tt>, <tt>DIP</tt>, <tt>RMS</tt>, <tt>CPHI</tt>, <tt>RMSA</tt>, <tt>PHI</tt>, <tt>PSI</tt>, <tt>HB3</tt>, <tt>HB4</tt>, <tt>HB5</tt> or <tt>CD222</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ev</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write a new 'trajectory' file for ED </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ev</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write a new 'trajectory' file for ED </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ahxstart</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> First residue in helix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ahxend</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Last residue in helix </TD></TD>
</TABLE>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> lie.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Elj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Lennard-Jones interaction between ligand and solvent </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Eqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Coulomb interaction between ligand and solvent </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Clj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.181</tt> </TD><TD> Factor in the LIE equation for Lennard-Jones component of energy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Cqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> Factor in the LIE equation for Coulomb component of energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Elj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Lennard-Jones interaction between ligand and solvent </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Eqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Coulomb interaction between ligand and solvent </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Clj</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.181 </tt> </TD><TD> Factor in the LIE equation for Lennard-Jones component of energy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Cqq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Factor in the LIE equation for Coulomb component of energy </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ligand</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Name of the ligand in the energy file </TD></TD>
</TABLE>
<P>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mean</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> dm.xpm</a></tt> </TD><TD> Output </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-frames</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> dmf.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1.5</tt> </TD><TD> trunc distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1.5 </tt> </TD><TD> trunc distance </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize distance in # levels </TD></TD>
</TABLE>
<P>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> mindist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-on</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> numcont.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="out.html">atm-pair.out</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic output file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> mindist.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> mindist.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">mindistres.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]max</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate *maximum* distance instead of minimum </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.6</tt> </TD><TD> Distance for contacts </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Split graph where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]matrix</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate half a matrix of group-group distances </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]max</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate *maximum* distance instead of minimum </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6 </tt> </TD><TD> Distance for contacts </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate minimum distance with periodic images </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of secondary groups to compute distance to a central group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Take periodic boundary conditions into account </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> interm.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf1.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf2.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> interm.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">rms-interm.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ninterm</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>11</tt> </TD><TD> Number of intermediates </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Corresponds to first generated structure (0 is input x0, see above) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Corresponds to last generated structure (1 is input x1, see above) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Corresponds to first generated structure (0 is input x0, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Corresponds to last generated structure (1 is input x1, see above) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares fit of the second to the first structure before interpolating </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>-endfit</tt>. An error estimate given, which is the difference
of the diffusion coefficients obtained from fits over the two halfs
of the fit interval.<p>
+There are three, mutually exclusive, options to determine different
+types of mean square displacement: <tt>-type</tt>, <tt>-lateral</tt>
+and <tt>-ten</tt>. Option <tt>-ten</tt> writes the full MSD tensor for
+each group, the order in the output is: trace xx yy zz yx zx zy.<p>
Option <tt>-mol</tt> plots the MSD for molecules, this implies
+With option <tt>-rmcomm</tt> center of mass motion can be removed.
+For trajectories produced with GROMACS this is usually not necessary
+as <a href="mdrun.html">mdrun</a> usually already removes the center of mass motion.
+When you use this option be sure that the whole system is stored
+in the trajectory file.<p>
<tt>-mw</tt>, i.e. for each inidividual molecule an diffusion constant
-is computed. When using an index file, it should contain molecule
-numbers instead of atom numbers.
+is computed for its center of mass. The chosen index group will
+be split into molecules.
+The diffusion coefficient is determined by linear regression of the MSD,
+where, unlike for the normal output of D, the times are weighted
+according to the number of restart point, i.e. short times have
+a higher weight. Also when <tt>-beginfit</tt>=-1,fitting starts at 0
+and when <tt>-endfit</tt>=-1, fitting goes to the end.
Using this option one also gets an accurate error estimate
-based on the statistics between individual molecules. Since one usually
-is interested in self-diffusion at infinite dilution this is probably
-the most useful number.<p>
+based on the statistics between individual molecules.
+Note that this diffusion coefficient and error estimate are only
+accurate when the MSD is completely linear between
+<tt>-beginfit</tt> and <tt>-endfit</tt>.<p>
+Option <tt>-<a href="pdb.html">pdb</a></tt> writes a <a href="pdb.html">pdb</a> file with the coordinates of the frame
+at time <tt>-tpdb</tt> with in the B-factor field the square root of
+the diffusion coefficient of the molecule.
+This option implies option <tt>-mol</tt>.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> msd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">diff_mol.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pdb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">diff_mol.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Compute diffusion coefficient in one direction: <tt>no</tt>, <tt>x</tt>, <tt>y</tt> or <tt>z</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-lateral</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Calculate the lateral diffusion in a plane perpendicular to: <tt>no</tt>, <tt>x</tt>, <tt>y</tt> or <tt>z</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ten</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the full tensor </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ngroup</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to calculate MSD for </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Mass weighted MSD </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-trestart</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 10</tt> </TD><TD> Time between restarting points in trajectory (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Start time for fitting the MSD (ps), -1 is 10% </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> End time for fitting the MSD (ps), -1 is 90% </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Mass weighted MSD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmcomm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove center of mass motion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tpdb</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The frame to use for option -<a href="pdb.html">pdb</a> (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trestart</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>10 </tt> </TD><TD> Time between restarting points in trajectory (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Start time for fitting the MSD (ps), -1 is 10% </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> End time for fitting the MSD (ps), -1 is 90% </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> hessian.mtx</a></tt> </TD><TD> Input </TD><TD> Hessian matrix </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenfreq.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Divide elements of Hessian by product of sqrt(mass) of involved atoms prior to diagonalization. This should be used for 'Normal Modes' analysis </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> First eigenvector to write away </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-last</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>50</tt> </TD><TD> Last eigenvector to write away </TD></TD>
</TABLE>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Input </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">ensemble.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">ensemble.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> Temperature in Kelvin </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Temperature in Kelvin </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Random seed, -1 generates a seed from time and pid </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-num</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Number of structures to generate </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-first</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> First eigenvector to use (-1 is select) </TD></TD>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmtraj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> nmtraj.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-v</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> nmtraj.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eignr</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> Eigenvector to use (first is 1) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> Temperature in Kelvin </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-amplitude</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.25</tt> </TD><TD> Amplitude for modes with eigenvalue<=0 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eignr</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>7</tt> </TD><TD> String of eigenvectors to use (first is 1) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-phases</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>0.0</tt> </TD><TD> String of phases (default is 0.0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-temp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> Temperature in Kelvin </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-amplitude</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.25 </tt> </TD><TD> Amplitude for modes with eigenvalue<=0 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nframes</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>30</tt> </TD><TD> Number of frames to generate </TD></TD>
</TABLE>
<P>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
order tensor component (specified by the -d option) is given and the
order parameter per slice is calculated as well. If -szonly is not
selected, all diagonal elements and the deuterium order parameter is
-given.
+given.<p>The tetrahedrality order parameters can be determined
+around an atom. Both angle an distance order parameters are calculated. See
+P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
+for more details.<br>
+
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> order.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> deuter.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-os</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sliced.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-Sg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sg-ang.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-Sk</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sk-dist.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: <tt>z</tt>, <tt>x</tt> or <tt>y</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Calculate order parameter as function of boxlength, dividing the box in #nr slices. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with -d) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]szonly</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only give Sz element of order tensor. (axis can be specified with -d) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]unsat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters. </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">potential.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> charge.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Z</tt> </TD><TD> Take the normal on the membrane in direction X, Y or Z. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-sl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Calculate potential as function of boxlength, dividing the box in #nr slices. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-cb</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard first #nr slices of box for integration </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ce</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Discard last #nr slices of box for integration </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tz</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Translate all coordinates <distance> in the direction of the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate spherical thingie </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tz</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Translate all coordinates <distance> in the direction of the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate spherical thingie </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to consider </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]correct</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Assume net zero charge of groups to improve accuracy </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>Discarding slices for integration should not be necessary.
</UL>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rama.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
is around the center of mass of a set of particles.
With both methods rdf's can also be calculated around axes parallel
to the z-axis with option <tt>-xy</tt>.<p>
-If a run input file is supplied (<tt>-s</tt>), exclusions defined
+The option <tt>-rdf</tt> sets the type of rdf to be computed.
+Default is for atoms or particles, but one can also select center
+of mass or geometry of molecules or residues. In all cases only
+the atoms in the index groups are taken into account.
+For molecules and/or the center of mass option a run input file
+is required.
+Other weighting than COM or COG can currently only be achieved
+by providing a run input file with different masses.
+Option <tt>-com</tt> also works in conjunction with <tt>-rdf</tt>.<p>If a run input file is supplied (<tt>-s</tt>) and <tt>-rdf</tt> is set
+to <tt>atom</tt>, exclusions defined
in that file are taken into account when calculating the rdf.
The option <tt>-cut</tt> is meant as an alternative way to avoid
intramolecular peaks in the rdf plot.
would eliminate all intramolecular contributions to the rdf.
Note that all atoms in the selected groups are used, also the ones
that don't have Lennard-Jones interactions.<p>
-Option <tt>-cn</tt> produces the cumulative number rdf.<p>To bridge the gap between theory and experiment structure factors can
+Option <tt>-cn</tt> produces the cumulative number rdf,
+i.e. the average number of particles within a distance r.<p>
+To bridge the gap between theory and experiment structure factors can
be computed (option <tt>-sq</tt>). The algorithm uses FFT, the gridspacing of which is determined by option <tt>-grid</tt>.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-sq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sq.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.002</tt> </TD><TD> Binwidth (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Use periodic boundary conditions for computing distances </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use only the x and y components of the distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Shortest distance (nm) to be considered </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.002 </tt> </TD><TD> Binwidth (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> RDF with respect to the center of mass of first group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rdf</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>atom</tt> </TD><TD> RDF type: <tt>atom</tt>, <tt>mol_com</tt>, <tt>mol_cog</tt>, <tt>res_com</tt> or <tt>res_cog</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions for computing distances. Without PBC the maximum range will be three times the larges box edge. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]norm</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize for volume and density </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xy</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use only the x and y components of the distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cut</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Shortest distance (nm) to be considered </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of secondary groups to compute RDFs around a central group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fade</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fade</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> From this distance onwards the RDF is tranformed by g'(r) = 1 + [g(r)-1] exp(-(r/fade-1)^2 to make it go to 1 smoothly. If fade is 0.0 nothing is done. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevel</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>20</tt> </TD><TD> Number of different colors in the diffraction image </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-startq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Starting q (1/nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 60</tt> </TD><TD> Ending q (1/nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-energy</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 12</tt> </TD><TD> Energy of the incoming X-ray (keV) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-startq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Starting q (1/nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>60 </tt> </TD><TD> Ending q (1/nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-energy</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>12 </tt> </TD><TD> Energy of the incoming X-ray (keV) </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
Option <tt>-fit</tt> controls the least-squares fitting of
the structures on <a href="top.html">top</a> of each other: complete fit (rotation and
translation), translation only, or no fitting at all.<p>
+Option <tt>-mw</tt> controls whether mass weighting is done or not.
+If you select the option (default) and
+supply a valid <a href="tpr.html">tpr</a> file masses will be taken from there,
+otherwise the masses will be deduced from the atommass.<a href="dat.html">dat</a> file in
+the GROMACS library directory. This is fine for proteins but not
+necessarily for other molecules. A default mass of 12.011 amu (Carbon)
+is assigned to unknown atoms. You can check whether this happend by
+turning on the <tt>-debug</tt> flag and inspecting the <a href="log.html">log</a> file.<p>
With <tt>-f2</tt>, the 'other structures' are taken from a second
trajectory, this generates a comparison matrix of one trajectory
versus the other.<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mir</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rmsdmir.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-what</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rmsd</tt> </TD><TD> Structural difference measure: <tt>rmsd</tt>, <tt>rho</tt> or <tt>rhosc</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> PBC check </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> PBC check </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rot+trans</tt> </TD><TD> Fit to reference structure: <tt>rot+trans</tt>, <tt>translation</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-prev</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Compare with previous frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Split graph where time is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]split</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Split graph where time is zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip2</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame to matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in comparison matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Minimum level in comparison matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in bond angle matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Minimum level in bond angle matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in comparison matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-min</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum level in comparison matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in bond angle matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Minimum level in bond angle matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mw</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use mass weighting for superposition </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>80</tt> </TD><TD> Number of levels in the matrices </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to compute RMS between </TD></TD>
</TABLE>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-equiv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html"> equiv.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">distrmsd.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>40</tt> </TD><TD> Discretize rms in # levels </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Maximum level in matrices </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> average distance over equivalent hydrogens </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Maximum level in matrices </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sumh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> average distance over equivalent hydrogens </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions
-after
first fitting to a reference frame.<p>
+after
(optionally) fitting to a reference frame.<p>
With option <tt>-oq</tt> the RMSF values are converted to B-factor
values, which are written to a <a href="pdb.html">pdb</a> file with the coordinates, of the
structure file, or of a <a href="pdb.html">pdb</a> file when <tt>-q</tt> is specified.
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> eiwit.pdb</a></tt> </TD><TD> Input, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oq</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> bfac.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate averages for each residue </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]res</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate averages for each residue </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aniso</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compute anisotropic termperature factors </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match. </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> rotacf.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use index doublets (vectors) for correlation function instead of triplets (planes) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Average over molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use index doublets (vectors) for correlation function instead of triplets (planes) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]aver</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Average over molecules </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_saltbr plots the difference between all combination of charged groups
+g_saltbr plots the distance between all combination of charged groups
as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg. the cut-off), then groups
that are never closer than that distance will not be plotted.<br>
-Output will be in a number of fixed filenames, min-min.<a href="xvg.html">xvg</a>,
min-plus.<a href="xvg.html">xvg</a>
+Output will be in a number of fixed filenames, min-min.<a href="xvg.html">xvg</a>,
plus-min.<a href="xvg.html">xvg</a>
and plus-plus.<a href="xvg.html">xvg</a>, or files for every individual ion-pair if selected
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1000</tt> </TD><TD> trunc distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use separate files for each interaction (may be MANY) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> trunc distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use separate files for each interaction (may be MANY) </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
generated (option <tt>-i</tt>)
which can be used to restrain surface atoms.<p>
By default, periodic boundary conditions are taken into account,
-this can be turned off using the <tt>-pbc</tt> option.
+this can be turned off using the <tt>-pbc</tt> option.<p>
+With the <tt>-tv</tt> option the total volume and density of the molecule can be
+computed.
+Please consider whether the normal probe radius is appropriate
+in this case or whether you would rather use e.g. 0. It is good
+to keep in mind that the results for volume and density are very
+approximate, in e.g. ice Ih one can easily fit water molecules in the
+pores which would yield too low volume, too high surface area and too
+high density.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> area.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-or</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> resarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">atomarea.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> volume.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">connelly.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html"> surfat.itp</a></tt> </TD><TD> Output, Opt. </TD><TD> Include file for topology </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-solsize</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.14</tt> </TD><TD> Radius of the solvent probe (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-probe</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.14 </tt> </TD><TD> Radius of the solvent probe (nm) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndots</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>24</tt> </TD><TD> Number of dots per sphere, more dots means more accuracy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.2</tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]f_index</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Determine from a group in the index file what are the hydrophobic atoms rather than from the charge </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Take periodicity into account </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.2 </tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]f_index</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Determine from a group in the index file what are the hydrophobic atoms rather than from the charge </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_angle.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sg_dist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-od1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">sg_dist1.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use periodic boundary conditions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Only one group compute angle between vector at time zero and time t </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the Z-axis as reference </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]one</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Only one group compute angle between vector at time zero and time t </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the Z-axis as reference </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sham</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-g_sham reads a number of <a href="xvg.html">xvg</a> files and analyzes data sets.
+g_sham makes multi-dimensional free-energy, enthalpy and entropy plots.
+g_sham reads one or more <a href="xvg.html">xvg</a> files and analyzes data sets.
+g_sham basic purpose is plotting Gibbs free energy landscapes
+(option <tt>-ls</tt>)
+by Bolzmann inverting multi-dimensional histograms (option <tt>-lp</tt>)
+but it can also
+make enthalpy (option <tt>-lsh</tt>) and entropy (option <tt>-lss</tt>)
+plots. The histograms can be made for any quantities the user supplies.
A line in the input file may start with a time
(see option <tt>-time</tt>) and any number of y values may follow.
Multiple sets can also be
All lines starting with # and @ are skipped.
<p>
Option <tt>-ge</tt> can be used to supply a file with free energies
-when the ensemble is not a Boltzmann ensemble, but has been biased
-by this free energy.
+when the ensemble is not a Boltzmann ensemble, but needs to be biased
+by this free energy. One free energy value is required for each
+(multi-dimensional) data point in the <tt>-f</tt> input.
+<p>
+Option <tt>-<a href="ene.html">ene</a></tt> can be used to supply a file with energies.
+These energies are used as a weighting function in the single
+histogram analysis method due to Kumar et. al. When also temperatures
+are supplied (as a second column in the file) an experimental
+weighting scheme is applied. In addition the vales
+are used for making enthalpy and entropy plots.
<p>
With option <tt>-dim</tt> dimensions can be gives for distances.
When a distance is 2- or 3-dimensional, the circumference or surface
sampled by two particles increases with increasing distance.
Depending on what one would like to show, one can choose to correct
-the free-energy for this volume effect.
+the histogram and free-energy for this volume effect.
The probability is normalized by r and r^2 for a dimension of 2 and 3
respectively.
+A value of -1 is used to indicate an angle in degrees between two
+vectors: a sin(angle) normalization will be applied.
Note that for angles between vectors the inner-product or cosine
is the natural quantity to use, as it will produce bins of the same
volume.
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ener.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-histo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> edist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> bindex.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-lp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> prob.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ls</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> gibbs.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-lsh</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html">enthalpy.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-lss</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> entropy.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Expect a time in the input </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to read from set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to read from set </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ttol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Tolerance on time in appropriate units (usually ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]time</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Expect a time in the input </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to read from set </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ttol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Tolerance on time in appropriate units (usually ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Read # sets seperated by & </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the derivative </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> Binwidth for the distribution </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sham</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Turn off energy weighting even if energies are given </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]d</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the derivative </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bw</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Binwidth for the distribution </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sham</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Turn off energy weighting even if energies are given </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-tsham</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>298.15</tt> </TD><TD> Temperature for single histogram analysis </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-pmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Minimum probability. Anything lower than this will be set to zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum probability. Anything lower than this will be set to zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dim</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Dimensions for distances, used for volume correction (max 3 values, dimensions > 3 will get the same value as the last) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ngrid</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>32 32 32</tt> </TD><TD> Number of bins for energy landscapes (max 3 values, dimensions > 3 will get the same value as the last) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xmin</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Minimum for the axes in energy landscape (see above for > 3 dimensions) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-xmax</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Maximum for the axes in energy landscape (see above for > 3 dimensions) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-gmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Maximum level in output, 0 is calculate </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>25</tt> </TD><TD> Number of levels for energy landscape from single histogram analysis </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum probability in output, default is calculate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-gmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum free energy in output, default is calculate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-emin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum enthalpy in output, default is calculate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-emax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum enthalpy in output, default is calculate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nlevels</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>25</tt> </TD><TD> Number of levels for energy landscape </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-mname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Legend label for the custom landscape </TD></TD>
</TABLE>
<P>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
reference positions to the first atom of each solvent molecule:<br>theta1: the angle with the vector from the first atom of the solvent
molecule to the midpoint between atoms 2 and 3.<br>
theta2: the angle with the normal of the solvent plane, defined by the
-same three atoms.<br>
+same three atoms, or when the option <tt>-v23</tt> is set
+the angle with the vector between atoms 2 and 3.<br>
The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
consist of 3 atoms per solvent molecule.
Only solvent molecules between <tt>-rmin</tt> and <tt>-rmax</tt> are
considered for <tt>-o</tt> and <tt>-no</tt> each frame.<p>
<tt>-o</tt>: distribtion of cos(theta1) for rmin<=r<=rmax.<p>
-<tt>-no</tt>: distribution of
3cos^2(theta2)-1 for rmin<=r<=rmax.<p>
+<tt>-no</tt>: distribution of
cos(theta2) for rmin<=r<=rmax.<p>
<tt>-ro</tt>: <cos(theta1)> and <3cos^2(theta2)-1> as a function of the
distance.<p>
<tt>-co</tt>: the sum over all solvent molecules within distance r
of cos(theta1) and 3cos^2(theta2)-1 as a function of r.<p>
+<tt>-rc</tt>: the distribution of the solvent molecules as a function of r
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sori.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-no</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> snor.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ro</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> sord.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-co</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> scum.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rc</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> scount.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Minimum distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.5</tt> </TD><TD> Maximum distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.02</tt> </TD><TD> Binwidth </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the center of mass as the reference postion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v23</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the vector between atoms 2 and 3 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum distance (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.5 </tt> </TD><TD> Maximum distance (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Binwidth for the cosine </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rbin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.02 </tt> </TD><TD> Binwidth for r (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules. </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">transcur.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-oa</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">tcaf_all.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate tcaf of molecules </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-wt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Exponential decay time for the TCAF fit weights </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate tcaf of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]k34</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Also use k=(3,0,0) and k=(4,0,0) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-wt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Exponential decay time for the TCAF fit weights </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<tt>-scale</tt>. To get the velocities or forces of one
frame set both <tt>-b</tt> and <tt>-e</tt> to the time of
desired frame. When averaging over frames you might need to use
-the <tt>-nojump</tt> option to obtain the correct average coordinates.<p>
+the <tt>-nojump</tt> option to obtain the correct average coordinates.
+If you select either of these option the average force and velocity
+for each atom are written to an <a href="xvg.html">xvg</a> file as well
+(specified with <tt>-av</tt> or <tt>-af</tt>).<p>
Option <tt>-vd</tt> computes a velocity distribution, i.e. the
norm of the vector is plotted. In addition in the same graph
the kinetic energy distribution is given.
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ox</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> coord.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oxt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> coord.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ov</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> veloc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ob</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> box.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-vd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> veldist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-cv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> veloc.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-cf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> force.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">all_veloc.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-af</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">all_force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot data for the com of each group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Index contains molecule numbers iso atom numbers </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot X-component </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot Y-component </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Plot Z-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot data for the com of each group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Index contains molecule numbers iso atom numbers </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nojump</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove jumps of atoms across the box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]x</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot X-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]y</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Y-component </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]z</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Plot Z-component </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ng</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of groups to consider </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Plot vector length </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Binwidth for velocity histogram (nm/ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>
0</tt> </TD><TD> Scale factor for <a href="pdb.html">pdb</a> output, 0 is autoscale </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]len</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Plot vector length </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Binwidth for velocity histogram (nm/ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>
0 </tt> </TD><TD> Scale factor for <a href="pdb.html">pdb</a> output, 0 is autoscale </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
g_velacc computes the velocity autocorrelation function.
-When the <tt>-s</tt> option is used, the momentum autocorrelation
+When the <tt>-m</tt> option is used, the momentum autocorrelation
function is calculated.<p>
With option <tt>-mol</tt> the momentum autocorrelation function of
molecules is calculated. In this case the index group should consist
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> vac.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate vac of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]m</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the momentum autocorrelation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]mol</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Calculate the momentum acf of molecules </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-acflen</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Length of the ACF, default is half the number of frames </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Normalize ACF </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]normalize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Normalize ACF </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-P</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Order of Legendre polynomial for ACF (0 indicates none): <tt>0</tt>, <tt>1</tt>, <tt>2</tt> or <tt>3</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt>, <tt>exp7</tt> or <tt>exp9</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ncskip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip N points in the output file of correlation functions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-beginfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Time where to begin the exponential fit of the correlation function </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-endfit</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Time where to end the exponential fit of the correlation function, -1 is till the end </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
2) Solvate a solute configuration, eg. a protein, in a bath of solvent
molecules. Specify <tt>-cp</tt> (solute) and <tt>-cs</tt> (solvent).
The box specified in the solute coordinate file (<tt>-cp</tt>) is used,
-unless <tt>-box</tt> is set, which also centers the solute.
-The program <tt><a href="editconf.html">editconf</a></tt> has more sophisticated options to change
-the box and center the solute.
+unless <tt>-box</tt> is set.
+If you want the solute to be centered in the box,
+the program <tt><a href="editconf.html">editconf</a></tt> has sophisticated options
+to change the box dimensions and center the solute.
Solvent molecules are removed from the box where the
distance between any atom of the solute molecule(s) and any atom of
the solvent molecule is less than the sum of the VanderWaals radii of
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> protein.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-cs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> spc216.gro</a></tt> </TD><TD> Input, Opt., Lib. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ci</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> insert.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> protein.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> spc216.gro</a></tt> </TD><TD> Input, Opt., Lib. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ci</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> insert.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> box size </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> no of extra molecules to insert </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-try</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> try inserting -nmol*-try times </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1997</tt> </TD><TD> random generator seed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.105</tt> </TD><TD> default vdwaals distance </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> thickness of optional water layer around solute </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-vdwd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.105 </tt> </TD><TD> default vdwaals distance </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-shell</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> thickness of optional water layer around solute </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxsol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> maximum number of solvent molecules to add if they fit in the box. If zero (default) this is ignored </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> keep velocities from input solute and solvent </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>Molecules must be whole in the initial configurations.
-<LI>At the moment -ci only works when inserting one molecule.
</UL>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-trj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-trj</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nbox</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>1 1 1</tt> </TD><TD> Number of boxes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Distance between boxes </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Random generator seed, if 0 generated from the time </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Randomly rotate conformations </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Random shuffling of molecules </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sort molecules on X coord </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Randomly rotate conformations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Random shuffling of molecules </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Sort molecules on X coord </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-block</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Divide the box in blocks on this number of cpus </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nmolat</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms per molecule, assumed to start from 0. If you set this wrong, it will screw up your system! </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-maxrot</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>90 90 90</tt> </TD><TD> Maximum random rotation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Renumber residues </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber residues </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>The program should allow for random displacement off lattice points.
</UL>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> out.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> genion.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-pot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html"> pot.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> In/Out, Opt. </TD><TD> Topology file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of positive ions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-pname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Na</tt> </TD><TD> Name of the positive ion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-pq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> Charge of the positive ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Charge of the positive ion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of negative ions </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nname</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>Cl</tt> </TD><TD> Name of the negative ion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nq</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Charge of the negative ion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.6</tt> </TD><TD> Minimum distance between ions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Charge of the negative ion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.6 </tt> </TD><TD> Minimum distance between ions </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]random</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use random placement of ions instead of based on potential. The rmin option should still work </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-seed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1993</tt> </TD><TD> Seed for random number generator </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.001</tt> </TD><TD> Scaling factor for the potential for -pot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Scaling factor for the potential for -pot </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-conc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Specify salt concentration (mol/liter). This will add sufficient ions to reach up to the specified concentration as computed from the volume of the cell in the input <a href="tpr.html">tpr</a> file. Overrides the -np and nn options. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]neutral</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> This option will add enough ions to neutralize the system. In combination with the concentration option a neutral system at a given salt concentration will be generated. </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
+<UL>
+<LI>Calculation of the potential is not reliable, therefore the <tt>-random</tt> option is now turned on by default.
+<LI>If you specify a salt concentration existing ions are not taken into account. In effect you therefore specify the amount of salt to be added.
+</UL>
+<P>
<hr>
<div ALIGN=RIGHT>
<font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Mon 29 Aug 2005</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<H3>Contents</H3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
gmxcheck reads a trajectory (<tt>.<a href="trj.html">trj</a></tt>, <tt>.<a href="trr.html">trr</a></tt> or
-<tt>.<a href="xtc.html">xtc</a></tt>) or an energy file (<tt>.<a href="ene.html">ene</a></tt> or <tt>.<a href="edr.html">edr</a></tt>)
+<tt>.<a href="xtc.html">xtc</a></tt>), an energy file (<tt>.<a href="ene.html">ene</a></tt> or <tt>.<a href="edr.html">edr</a></tt>)
+or an index file (<tt>.<a href="ndx.html">ndx</a></tt>)
and prints out useful information about them.<p>
Option <tt>-c</tt> checks for presence of coordinates,
velocities and box in the file, for close contacts (smaller than
<tt>.<a href="tpa.html">tpa</a></tt>) files
when both <tt>-s1</tt> and <tt>-s2</tt> are supplied.
Similarly a pair of trajectory files can be compared (using the <tt>-f2</tt>
-option), or a pair of energy files (using the <tt>-e2</tt> option).
+option), or a pair of energy files (using the <tt>-e2</tt> option).<p>
+For free energy simulations the A and B state topology from one
+run input file can be compared with options <tt>-s1</tt> and <tt>-ab</tt>.<p>
+In case the <tt>-m</tt> flag is given a LaTeX file will be written
+consisting a rough outline for a methods section for a paper.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top1.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top2.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener2.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s1</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top1.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> top2.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e2</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener2.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-m</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="tex.html"> doc.tex</a></tt> </TD><TD> Output, Opt. </TD><TD> LaTeX file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-vdwfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.8</tt> </TD><TD> Fraction of sum of VdW radii used as warning cutoff </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bonlo</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.4</tt> </TD><TD> Min. fract. of sum of VdW radii for bonded atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bonhi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.7</tt> </TD><TD> Max. fract. of sum of VdW radii for bonded atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.001</tt> </TD><TD> Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-vdwfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8 </tt> </TD><TD> Fraction of sum of VdW radii used as warning cutoff </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bonlo</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.4 </tt> </TD><TD> Min. fract. of sum of VdW radii for bonded atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bonhi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.7 </tt> </TD><TD> Max. fract. of sum of VdW radii for bonded atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.001 </tt> </TD><TD> Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ab</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Compare the A and B topology from one file </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-lastener</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. </TD></TD>
</TABLE>
<P>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Gmxdemo</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
file (<tt>.<a href="ene.html">ene</a></tt>/<tt>.<a href="edr.html">edr</a></tt>) and prints that to standard
output in a readable format. This program is essential for
checking your run input file in case of problems.<p>
+When requesting to dump a topology file the program will dump
+the processed topology, since not all original information is maintained
+in <a href="tpr.html">tpr</a> files.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD> Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html"> state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-om</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> grompp.mdp</a></tt> </TD><TD> Output, Opt. </TD><TD> <a href="grompp.html">grompp</a> input file with MD parameters </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology) </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
warnings when they do not match the atom names in the topology.
Note that the atom names are irrelevant for the simulation as
only the atom types are used for generating interaction parameters.<p>
-grompp calls the c-preprocessor to resolve includes, macros
-etcetera. To specify a macro-preprocessor other than /lib/cpp
-(such as m4)
+grompp calls a preprocessor to resolve includes, macros
+etcetera. By default we use the cpp in your path. To specify a different macro-preprocessor (e.g. m4) or alternative location
you can put a line in your parameter file specifying the path
-to that cpp. Specifying <tt>-pp</tt> will get the pre-processed
+to that program. Specifying <tt>-pp</tt> will get the pre-processed
topology file written out.<p>
If your system does not have a c-preprocessor, you can still
use grompp, but you do not have access to the features
when constraints are present in the system.
If you want to continue a crashed run, it is
easier to use <tt><a href="tpbconv.html">tpbconv</a></tt>.<p>
-When preparing an input file for parallel <tt><a href="mdrun.html">mdrun</a></tt> it may
-be advantageous to partition the simulation system over the
-nodes in a way in which each node has a similar amount of
-work. The -shuffle option does just that. For a single protein
-in water this does not make a difference, however for a system where
-you have many copies of different molecules (e.g. liquid mixture
-or membrane/water system) the option is definitely a must.
-The output trajectories will also be shuffled. <tt>grompp</tt> writes
-an index file (option <tt>-deshuf</tt>) which can be used with
-<tt><a href="trjconv.html">trjconv</a></tt> to deshuffle the trajectories.<p>
-A further optimization for parallel systems is the <tt>-sort</tt>
-option which sorts molecules according to coordinates. This must
-always be used in conjunction with <tt>-shuffle</tt>, however
-sorting also works when you have only one molecule type.<p>
Using the <tt>-morse</tt> option grompp can convert the harmonic bonds
in your topology to morse potentials. This makes it possible to break
bonds. For this option to work you need an extra file in your $GMXLIB
with dissociation energy. Use the -debug option to get more information
-on the workings of this option (look for MORSE in the grompp.log file
+on the workings of this option (look for MORSE in the grompp.<a href="log.html">log</a> file
using less or something like that).<p>
By default all bonded interactions which have constant energy due to
virtual site constructions will be removed. If this constant energy is
of the <tt>mdout.<a href="mdp.html">mdp</a></tt> file, this contains comment lines, as well as
the input that <tt>grompp</tt> has read. If in doubt you can start grompp
with the <tt>-debug</tt> option which will give you more information
-in a file called grompp.log (along with real debug info). Finally, you
+in a file called grompp.<a href="log.html">log</a> (along with real debug info). Finally, you
can see the contents of the run input file with the <tt><a href="gmxdump.html">gmxdump</a></tt>
program.
<P>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> grompp.mdp</a></tt> </TD><TD> Input, Opt. </TD><TD> grompp input file with MD parameters </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html"> mdout.mdp</a></tt> </TD><TD> Output </TD><TD> grompp input file with MD parameters </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-rb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-deshuf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> deshuf.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> Input </TD><TD> Topology file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-pp</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html">processed.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Output </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Output </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-t</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Be loud and noisy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Take frame at or first after this time. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Generate statusfile for # nodes </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]shuffle</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Shuffle molecules over nodes </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Sort molecules according to X coordinate </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmvsbds</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Remove constant bonded interactions with virtual sites </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-load</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Releative load capacity of each node on a parallel machine. Be sure to use quotes around the string, which should contain a number for each node </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>10</tt> </TD><TD> Number of warnings after which input processing stops </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]check14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove 1-4 interactions without Van der Waals </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Renumber atomtypes and minimize number of atomtypes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Take frame at or first after this time. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]rmvsbds</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Remove constant bonded interactions with virtual sites </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxwarn</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of allowed warnings during input processing </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zero</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set parameters for bonded interactions without defaults to zero instead of generating an error </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]renum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Renumber atomtypes and minimize number of atomtypes </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
</TABLE>
<P>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_edi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-<tt>make_<a href="edi.html">edi</a></tt> generates an
ED-sampling input file to be used with <a href="mdrun.html">mdrun</a>
+<tt>make_<a href="edi.html">edi</a></tt> generates an
essential dynamics (ED) sampling input file to be used with <a href="mdrun.html">mdrun</a>
based on eigenvectors of a covariance matrix (<tt><a href="g_covar.html">g_covar</a></tt>) or from a
-
Normal Modes anaysis (<tt><a href="g_nmeig.html">g_nmeig</a></tt>).
-ED-sampling can be used to manipulate the position along collective coordinates
+
normal modes anaysis (<tt><a href="g_nmeig.html">g_nmeig</a></tt>).
+ED sampling can be used to manipulate the position along collective coordinates
(eigenvectors) of (biological) macromolecules during a simulation. Particularly,
it may be used to enhance the sampling efficiency of MD simulations by stimulating
the system to explore new regions along these collective coordinates. A number
of different algorithms are implemented to drive the system along the eigenvectors
(<tt>-linfix</tt>, <tt>-linacc</tt>, <tt>-radfix</tt>, <tt>-radacc</tt>, <tt>-radcon</tt>),
to keep the position along a certain (set of) coordinate(s) fixed (<tt>-linfix</tt>),
-or to only monitor the projections of the positions, velocities and forces onto
-these coordinates(<tt>-mon</tt>).<p>References:<br>
+or to only monitor the projections of the positions onto
+these coordinates
(<tt>-mon</tt>).<p>References:<br>
A. Amadei, A.B.M. Linssen, B.L. de Groot, D.M.F. van Aalten and
H.J.C. Berendsen; An efficient method for sampling the essential subspace
of proteins., J. Biomol. Struct. Dyn. 13:615-626 (1996)<br>
PROTEINS: Struct. Funct. Gen. 26: 314-322 (1996)
<p>You will be prompted for one or more index groups that correspond to the eigenvectors,
reference structure, target positions, etc.<p>
-<tt>-mon</tt>: monitor projections of
x, v and f onto selected eigenvectors.<p>
+<tt>-mon</tt>: monitor projections of
the coordinates onto selected eigenvectors.<p>
<tt>-linfix</tt>: perform fixed-step linear expansion along selected eigenvectors.<p>
<tt>-linacc</tt>: perform acceptance linear expansion along selected eigenvectors.
(steps in the desired directions will be accepted, others will be rejected).<p>
Note: by default the starting MD structure will be taken as origin of the first
expansion cycle for radius expansion. If <tt>-ori</tt> is specified, you will be able
to read in a structure file that defines an external origin.<p><tt>-radcon</tt>: perform acceptance radius contraction along selected eigenvectors
-towards a target structure specified with <tt>-tar</tt>.
NOTE: each eigenvector can be selected only once. <p><tt>-outfrq</tt>: frequency (in steps) of writing out projections etc.<p>
+towards a target structure specified with <tt>-tar</tt>.
<p>NOTE: each eigenvector can be selected only once. <p><tt>-outfrq</tt>: frequency (in steps) of writing out projections etc. to .<a href="edo.html">edo</a> file<p>
<tt>-slope</tt>: minimal slope in acceptance radius expansion. A new expansion
cycle will be started if the spontaneous increase of the radius (in nm/step)
is less than the value specified.<p><tt>-maxedsteps</tt>: maximum number of steps per cycle in radius expansion
before a new cycle is started.<p>Note on the parallel implementation: since ED sampling is a 'global' thing
-(collective coordinates etc), at least on the 'protein' side, ED sampling
-is not very parallel-friendly from an implentation point of view (it would
-require much extra communication to fully parallelize the algorithms).
-Fortunately, however, a typical parallel protein simulation in gromacs has
-most or all protein coordinates on one processor (the master) and has only
-other atoms (solvent, lipid, ions etc) on the other processors. With such a
-setup, ED sampling will still work. If the atoms over which ED sampling should
-be performed are spread over multiple processors, a fatal error will result.<p>All output of <a href="mdrun.html">mdrun</a> (specify with -eo) is written to a .<a href="edo.html">edo</a> file (some extra
-information is written to the log file of <a href="mdrun.html">mdrun</a> too, actually). The .<a href="edo.html">edo</a> format
-is a simple ASCII file that should be easy to parse with standard unix tools
-like awk. A script (parse_<a href="edo.html">edo</a>) can be downloaded from contribution section at
- www.gromacs.org to extract information from the
-.<a href="edo.html">edo</a> files for your convinience. In short, the header defines which information
-can be expected in the rest of the .<a href="edo.html">edo</a> file. After the header, per step the
-following information is present: <p>
+(collective coordinates etc.), at least on the 'protein' side, ED sampling
+is not very parallel-friendly from an implentation point of view. Because
+parallel ED requires much extra communication, expect the performance to be
+lower as in a free MD simulation, especially on a large number of nodes. <p>
+All output of <a href="mdrun.html">mdrun</a> (specify with -eo) is written to a .<a href="edo.html">edo</a> file. In the output
+file, per OUTFRQ step the following information is present: <p>
* the step number<br>
-* RMSD (for atoms in fitting prior to calculating ED constr.)<br>
+* the number of the ED dataset. (Note that you can impose multiple ED constraints in
+a single simulation - on different molecules e.g. - if several .<a href="edi.html">edi</a> files were concatenated
+first. The constraints are applied in the order they appear in the .<a href="edi.html">edi</a> file.) <br>
+* RMSD (for atoms involved in fitting prior to calculating the ED constraints)<br>
* projections of the positions onto selected eigenvectors<br>
-* projections of the velocities onto selected eigenvectors<br>
-* projections of the forces onto selected eigenvectors
-<p>
-All projections are in the same order as in the header, so if you have e.g.
-2 groups (say one group over which acceptance radius expansion is performed,
-and another for which the projections are merely monitored) then you first
-get the position projections for each of the 2 groups, then the velocities
-and then the forces. Radii are not explicitly written to the .<a href="edo.html">edo</a> file, as
-they can be readily projected back from the positions. Alternatively, radii
-may be 'grepped from the log file.
<p><p>
FLOODING:<p>
with -flood you can specify which eigenvectors are used to compute a flooding potential,
which will lead to extra forces expelling the structure out of the region described
-by the covariance matrix. if you switch -restrain the potential is inverted and the structure
-is kept in that region
+by the covariance matrix. If you switch -restrain the potential is inverted and the structure
+is kept in that region.
<p>
-the origin is normally the average structure stored in the eigvec.<a href="trr.html">trr</a> file
-it can be changed with -ori to an arbitrary position in configurational space
-with -tau , -deltaF0 and -Eflnull you control the flooding strength
-Efl is the flooding strength, it is updated according to the rule of adaptive flooding
-tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth)
-deltaF0 is the flooding strength you want to reach after tau ps of simulation
-to use constant Efl set -tau to zero
+The origin is normally the average structure stored in the eigvec.<a href="trr.html">trr</a> file.
+It can be changed with -ori to an arbitrary position in configurational space.
+With -tau, -deltaF0 and -Eflnull you control the flooding behaviour.
+Efl is the flooding strength, it is updated according to the rule of adaptive flooding.
+Tau is the time constant of adaptive flooding, high tau means slow adaption (i.e. growth).
+DeltaF0 is the flooding strength you want to reach after tau ps of simulation.
+To use constant Efl set -tau to zero.
<p>
-alpha is a fudge parameter to control the width of the flooding potential. A value of 2 has been found
-to give good results for most standard cases in flooding of proteins
-alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
-increase, this is mimicked by alpha>1for restraining alpha<1 can give you smaller width in the restraining potentialRESTART and FLOODING:
+to give good results for most standard cases in flooding of proteins.
+Alpha basically accounts for incomplete sampling, if you sampled further the width of the ensemble would
+increase, this is mimicked by alpha>1.
+For restraining alpha<1 can give you smaller width in the restraining potential.
+<p>
+RESTART and FLOODING:
If you want to restart a crashed flooding simulation please find the values deltaF and Efl in
-the output file and write them with your texteditor into the .<a href="edi.html">edi</a> file under DELTA_F0 and EFL_NULL
+the output file and manually put them into the .<a href="edi.html">edi</a> file under DELTA_F0 and EFL_NULL.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">eigenvec.trr</a></tt> </TD><TD> Input </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eig</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">eigenval.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-tar</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> target.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ori</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> origin.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tar</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> target.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ori</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> origin.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Output </TD><TD> ED sampling input </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-mon</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for projections of x, v and f (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-mon</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for projections of x (e.g. 1,2-5,9) or 1-100:10 means 1 11 21 31 ... 91 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linfix</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for fixed increment linear sampling </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linacc</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance linear sampling </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-flood</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for flooding </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radfix</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for fixed increment radius expansion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radacc</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance radius expansion </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-radcon</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for acceptance radius contraction </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-flood</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Indices of eigenvectors for flooding </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-outfrq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> freqency (in steps) of writing output in .<a href="edo.html">edo</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-slope</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> minimal slope in acceptance radius expamsion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-maxedsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> max nr of steps per cycle </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deltaF0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 150</tt> </TD><TD> target destabilization energy - used for flooding </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-deltaF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> start deltaF with this parameter - default 0, i.g. nonzero values only needed for restart </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tau</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.1</tt> </TD><TD> coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-eqsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> number of steps to run without any perturbations </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-Eflnull</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> this is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 300</tt> </TD><TD> T is temperature, the value is needed if you want to do flooding </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-alpha</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1</tt> </TD><TD> scale width of gaussian flooding potential with alpha^2 </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-outfrq</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>100</tt> </TD><TD> Freqency (in steps) of writing output in .<a href="edo.html">edo</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-slope</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimal slope in acceptance radius expansion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxedsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Max nr of steps per cycle </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-deltaF0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>150 </tt> </TD><TD> Target destabilization energy - used for flooding </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-deltaF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start deltaF with this parameter - default 0, i.e. nonzero values only needed for restart </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tau</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.1 </tt> </TD><TD> Coupling constant for adaption of flooding strength according to deltaF0, 0 = infinity i.e. constant flooding strength </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-eqsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Number of steps to run without any perturbations </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-Eflnull</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> This is the starting value of the flooding strength. The flooding strength is updated according to the adaptive flooding scheme. To use a constant flooding strength use -tau 0. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>300 </tt> </TD><TD> T is temperature, the value is needed if you want to do flooding </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-alpha</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1 </tt> </TD><TD> Scale width of gaussian flooding potential with alpha^2 </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-linstep</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Stepsizes (nm/step) for fixed increment linear sampling (put in quotes! "1.0 2.3 5.1 -3.1") </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-accdir</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Directions for acceptance linear sampling - only sign counts! (put in quotes! "-1 +1 -1.1") </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-radstep</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Stepsize (nm/step) for fixed increment radius expansion </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]restrain</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]hesse</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> the eigenvectors and eigenvalues are from a Hesse matrix </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]harmonic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> the eigenvalues are interpreted as spring constant </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-radstep</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Stepsize (nm/step) for fixed increment radius expansion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]restrain</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the flooding potential with inverted sign -> effects as quasiharmonic restraining potential </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]hessian</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvectors and eigenvalues are from a Hessian matrix </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]harmonic</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> The eigenvalues are interpreted as spring constant </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt., Mult. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Output </TD><TD> Index file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-natoms</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> set number of atoms (default: read from coordinate or index file) </TD></TD>
</TABLE>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<P> Follow <a href="mdp_opt.html">this link</a> for a detailed description of the options</a>. </P>
<TD WIDTH=116>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdp options</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p> </p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
The mdrun program is the main computational chemistry engine
within GROMACS. Obviously, it performs Molecular Dynamics simulations,
-but it can also perform Brownian Dynamics and Langevin Dynamics
-as well as Conjugate Gradient or Steepest Descents energy minimization.
+but it can also perform Stochastic Dynamics, Energy Minimization,
+test particle insertion or (re)calculation of energies.
Normal mode analysis is another option. In this case mdrun
builds a Hessian matrix from single conformation.
For usual Normal Modes-like calculations, make sure that
-the structure provided is properly energy-minimised.
-The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.<p>The mdrun program reads the run input file (<tt>-s</tt>) and distributes the
-topology over nodes if needed. The coordinates are passed
-around, so that computations can begin.
-First a neighborlist is made, then the forces are computed.
-The forces are globally summed, and the velocities and
-positions are updated. If necessary shake is performed to constrain
-bond lengths and/or bond angles.
-Temperature and Pressure can be controlled using weak coupling to a
-bath.<p>
-mdrun produces at least three output file, plus one log file
-(<tt>-g</tt>) per node.
+the structure provided is properly energy-minimized.
+The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.<p>
+The mdrun program reads the run input file (<tt>-s</tt>)
+and distributes the topology over nodes if needed.
+mdrun produces at least four output files.
+A single <a href="log.html">log</a> file (<tt>-g</tt>) is written, unless the option
+<tt>-seppot</tt> is used, in which case each node writes a <a href="log.html">log</a> file.
The trajectory file (<tt>-o</tt>), contains coordinates, velocities and
optionally forces.
The structure file (<tt>-c</tt>) contains the coordinates and
velocities of the last step.
The energy file (<tt>-e</tt>) contains energies, the temperature,
-pressure, etc, a lot of these things are also printed in the log file
-of node 0.
+pressure, etc, a lot of these things are also printed in the <a href="log.html">log</a> file.
Optionally coordinates can be written to a compressed trajectory file
(<tt>-x</tt>).<p>
-When running in parallel with PVM or an old version of MPI the
-<tt>-np</tt> option must be given to indicate the number of
-nodes.<p>
The option <tt>-dgdl</tt> is only used when free energy perturbation is
turned on.<p>
+When mdrun is started using MPI with more than 1 node, parallelization
+is used. By default domain decomposition is used, unless the <tt>-pd</tt>
+option is set, which selects particle decomposition.<p>
+With domain decomposition, the spatial decomposition can be set
+with option <tt>-dd</tt>. By default mdrun selects a good decomposition.
+The user only needs to change this when the system is very inhomogeneous.
+Dynamic load balancing is set with the option <tt>-dlb</tt>,
+which can give a significant performance improvement,
+especially for inhomogeneous systems. The only disadvantage of
+dynamic load balancing is that runs are no longer binary reproducible,
+but in most cases this is not important.
+By default the dynamic load balancing is automatically turned on
+when the measured performance loss due to load imbalance is 5% or more.
+At low parallelization these are the only important options
+for domain decomposition.
+At high parallelization the options in the next two sections
+could be important for increasing the performace.
+<p>
+When PME is used with domain decomposition, separate nodes can
+be assigned to do only the PME mesh calculation;
+this is computationally more efficient starting at about 12 nodes.
+The number of PME nodes is set with option <tt>-npme</tt>,
+this can not be more than half of the nodes.
+By default mdrun makes a guess for the number of PME
+nodes when the number of nodes is larger than 11 or performance wise
+not compatible with the PME grid x dimension.
+But the user should optimize npme. Performance statistics on this issue
+are written at the end of the <a href="log.html">log</a> file.
+For good load balancing at high parallelization,
+npme should be divisible by the number of PME nodes
+<p>
+This section lists all options that affect the domain decomposition.
+<br>
+Option <tt>-rdd</tt> can be used to set the required maximum distance
+for inter charge-group bonded interactions.
+Communication for two-body bonded interactions below the non-bonded
+cut-off distance always comes for free with the non-bonded communication.
+Atoms beyond the non-bonded cut-off are only communicated when they have
+missing bonded interactions; this means that the extra cost is minor
+and nearly indepedent of the value of <tt>-rdd</tt>.
+With dynamic load balancing option <tt>-rdd</tt> also sets
+the lower limit for the domain decomposition cell sizes.
+By default <tt>-rdd</tt> is determined by mdrun based on
+the initial coordinates. The chosen value will be a balance
+between interaction range and communication cost.
+<br>
+When inter charge-group bonded interactions are beyond
+the bonded cut-off distance, mdrun terminates with an error message.
+For pair interactions and tabulated bonds
+that do not generate exclusions, this check can be turned off
+with the option <tt>-noddcheck<tt>.
+<br>
+When constraints are present, option <tt>-rcon</tt> influences
+the cell size limit as well.
+Atoms connected by NC constraints, where NC is the LINCS order plus 1,
+should not be beyond the smallest cell size. A error message is
+generated when this happens and the user should change the decomposition
+or decrease the LINCS order and increase the number of LINCS iterations.
+By default mdrun estimates the minimum cell size required for P-LINCS
+in a conservative fashion. For high parallelization it can be useful
+to set the distance required for P-LINCS with the option <tt>-rcon</tt>.
+<br>
+The <tt>-dds</tt> option sets the minimum allowed x, y and/or z scaling
+of the cells with dynamic load balancing. mdrun will ensure that
+the cells can scale down by at least this factor. This option is used
+for the automated spatial decomposition (when not using <tt>-dd</tt>)
+as well as for determining the number of grid pulses, which in turn
+sets the minimum allowed cell size. Under certain circumstances
+the value of <tt>-dds</tt> might need to be adjusted to account for
+high or low spatial inhomogeneity of the system.
+<p>
+The option <tt>-nosum</tt> can be used to only sum the energies
+at every neighbor search step and energy output step.
+This can improve performance for highly parallel simulations
+where this global communication step becomes the bottleneck.
+For a global thermostat and/or barostat the temperature
+and/or pressure will also only be updated every nstlist steps.
+With this option the energy file will not contain averages and
+fluctuations over all integration steps.<p>
With <tt>-rerun</tt> an input trajectory can be given for which
forces and energies will be (re)calculated. Neighbor searching will be
performed for every frame, unless <tt>nstlist</tt> is zero
<tt>.<a href="mdp.html">mdp</a></tt> file the <tt>-table</tt> option is used to pass mdrun
a formatted table with potential functions. The file is read from
either the current directory or from the GMXLIB directory.
-A number of preformatted tables are presented in the GMXLIB dir,
+A number of pre-formatted tables are presented in the GMXLIB dir,
for 6-8, 6-9, 6-10, 6-11, 6-12 Lennard Jones potentials with
normal Coulomb.
-When pair interactions are present a seperate table for pair interaction
+When pair interactions are present a separate table for pair interaction
functions is read using the <tt>-tablep</tt> option.<p>
+When tabulated bonded functions are present in the topology,
+interaction functions are read using the <tt>-tableb</tt> option.
+For each different tabulated interaction type the table file name is
+modified in a different way: before the file extension an underscore is
+appended, then a b for bonds, an a for angles or a d for dihedrals
+and finally the table number of the interaction type.<p>
The options <tt>-pi</tt>, <tt>-po</tt>, <tt>-pd</tt>, <tt>-pn</tt> are used
for potential of mean force calculations and umbrella sampling.
See manual.<p>
With <tt>-multi</tt> multiple systems are simulated in parallel.
-As many (single node) input files are required as the number of nodes.
-The node number is appended to the run input and each output filename,
+As many input files are required as the number of systems.
+The system number is appended to the run input and each output filename,
for instance topol.<a href="tpr.html">tpr</a> becomes topol0.<a href="tpr.html">tpr</a>, topol1.<a href="tpr.html">tpr</a> etc.
-The main use of this option is for NMR refinement: when distance
+The number of nodes per system is the total number of nodes
+divided by the number of systems.
+One use of this option is for NMR refinement: when distance
or orientation restraints are present these can be ensemble averaged
over all the systems.<p>
With <tt>-replex</tt> replica exchange is attempted every given number
-of steps. This option implies <tt>-multi</tt>, see above.
+of steps. The number of replicas is set with the <tt>-multi</tt> option,
+see above.
All run input files should use a different coupling temperature,
the order of the files is not important. The random seed is set with
<tt>-reseed</tt>. The velocities are scaled and neighbor searching
is performed after every exchange.<p>
Finally some experimental algorithms can be tested when the
appropriate options have been given. Currently under
-investigation are: polarizibility, glass simulations
-and X-Ray bombardments.<p>
+investigation are: polarizability, glass simulations
+and X-Ray bombardments.
+<p>
+The option <tt>-pforce</tt> is useful when you suspect a simulation
+crashes due to too large forces. With this option coordinates and
+forces of atoms with a force larger than a certain value will
+be printed to stderr.
+<p>
+Checkpoints containing the complete state of the system are written
+at regular intervals (option <tt>-cpt</tt>) to the file <tt>-cpo</tt>,
+unless option <tt>-cpt</tt> is set to -1.
+A simulation can be continued by reading the full state from file
+with option <tt>-cpi</tt>. This option is intelligent in the way that
+if no checkpoint file is found, Gromacs just assumes a normal run and
+starts from the first step of the <a href="tpr.html">tpr</a> file.
+<p>
+With checkpointing you can also use the option <tt>-append</tt> to
+just continue writing to the previous output files. This is not
+enabled by default since it is potentially dangerous if you move files,
+but if you just leave all your files in place and restart mdrun with
+exactly the same command (with options <tt>-cpi</tt> and <tt>-append</tt>)
+the result will be the same as from a single run. The contents will
+be binary identical (unless you use dynamic load balancing),
+but for technical reasons there might be some extra energy frames when
+using checkpointing (necessary for restarts without appending).
+<p>
+With option <tt>-maxh</tt> a simulation is terminated and a checkpoint
+file is written at the first neighbor search step where the run time
+exceeds <tt>-maxh</tt>*0.99 hours.
+<p>
When mdrun receives a TERM signal, it will set nsteps to the current
-step plus one. When mdrun receives a USR1 signal, it will set nsteps
-to the next multiple of nstxout after the current step.
+step plus one. When mdrun receives a USR1 signal, it will stop after
+the next neighbor search step (with nstlist=0 at the next step).
In both cases all the usual output will be written to file.
When running with MPI, a signal to one of the mdrun processes
is sufficient, this signal should not be sent to mpirun or
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Output </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-x</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xtc.html"> traj.xtc</a></tt> </TD><TD> Output, Opt. </TD><TD> Compressed trajectory (portable xdr format) </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> confout.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Output </TD><TD> Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html"> state.cpt</a></tt> </TD><TD> Input, Opt. </TD><TD> Checkpoint file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cpo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="cpt.html"> state.cpt</a></tt> </TD><TD> Output, Opt. </TD><TD> Checkpoint file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> confout.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Output </TD><TD> Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html"> md.log</a></tt> </TD><TD> Output </TD><TD> Log file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dgdl</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> dgdl.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-field</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> field.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-table</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tablep</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tablep.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tableb</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> table.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-tpi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpi.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-tpid</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> tpidist.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html"> sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html"> sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html"> wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pull.ppa</a></tt> </TD><TD> Input, Opt. </TD><TD> Pull parameters </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pullout.ppa</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull parameters </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdo.html"> pull.pdo</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull data output </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-pn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> pull.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-px</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullx.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-pf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> pullf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html"> nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-dn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> dipole.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-deffnm</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Set the default filename for all file options </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-np</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of nodes, must be the same as used for <a href="grompp.html">grompp</a> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-nt</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of threads to start on each node </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Be loud and noisy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Write a compact log file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sepdvdl</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the log file(s) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]multi</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do multiple simulations in parallel (only with -np > 1) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pd</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use particle decompostion </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dd</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Domain decomposition grid, 0 is optimize </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-npme</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Number of separate nodes to be used for PME, -1 is guess </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ddorder</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>interleave</tt> </TD><TD> DD node order: <tt>interleave</tt>, <tt>pp_pme</tt> or <tt>cartesian</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ddcheck</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Check for all bonded interactions with DD </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rdd</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> The maximum distance for bonded interactions with DD (nm), 0 is determine from initial coordinates </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rcon</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum distance for P-LINCS (nm), 0 is estimate </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dlb</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>auto</tt> </TD><TD> Dynamic load balancing (with DD): <tt>auto</tt>, <tt>no</tt> or <tt>yes</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dds</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.8 </tt> </TD><TD> Minimum allowed dlb scaling of the DD cell size </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sum</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sum the energies at every step </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be loud and noisy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]compact</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Write a compact <a href="log.html">log</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]seppot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write separate V and dVdl terms for each interaction type and node to the <a href="log.html">log</a> file(s) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pforce</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Print all forces larger than this (kJ/mol nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]reprod</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Try to avoid optimizations that affect binary reproducibility </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cpt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>15 </tt> </TD><TD> Checkpoint interval (minutes) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]append</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Append to previous output files when restarting from checkpoint </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-maxh</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Terminate after 0.99 times this time (hours) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-multi</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Do multiple simulations in parallel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-replex</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Attempt replica exchange every # steps </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-reseed</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Seed for replica exchange, -1 is generate a seed </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]glas</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do glass simulation with special long range corrections </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]glas</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do glass simulation with special long range corrections </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
</TABLE>
<P>
<hr>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Methanol</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Methanol+Water</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> angle.ndx</a></tt> </TD><TD> Output </TD><TD> Index file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle: <tt>angle</tt>, <tt><a href="g96.html">g96</a>-angle</tt>, <tt>dihedral</tt>, <tt>improper</tt>, <tt>ryckaert-bellemans</tt> or <tt>phi-psi</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle: <tt>angle</tt>, <tt>dihedral</tt>, <tt>improper</tt> or <tt>ryckaert-bellemans</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]hyd</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Include angles with atoms with mass < 1.5 </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>ngmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>Balls option does not work
<LI>Some times dumps core without a good reason
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> eiwit.pdb</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Output </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> eiwit.pdb</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Output </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-p</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> topol.top</a></tt> </TD><TD> Output </TD><TD> Topology file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-i</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="itp.html"> posre.itp</a></tt> </TD><TD> Output </TD><TD> Include file for topology </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> clean.ndx</a></tt> </TD><TD> Output, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> clean.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-q</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> clean.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Merge chains into one molecule definition </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]merge</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Merge chains into one molecule definition </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Force field, interactive by default. Use -h for information. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-water</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>spc</tt> </TD><TD> Water model to use: with GROMOS we recommend SPC, with OPLS, TIP4P: <tt>spc</tt>, <tt>spce</tt>, <tt>tip3p</tt>, <tt>tip4p</tt>, <tt>tip5p</tt> or <tt>f3c</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Set the next 6 options to interactive </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive SS bridge selection </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive termini selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Lysine selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Aspartic Acid selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Glutamic Acid selection, iso charged </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 135</tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.3</tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Ignore hydrogen atoms that are in the <a href="pdb.html">pdb</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]missing</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Continue when atoms are missing, dangerous </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Be slightly more verbose in messages </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-posrefc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1000</tt> </TD><TD> Force constant for position restraints </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]inter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the next 8 options to interactive </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ss</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive SS bridge selection </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive termini selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]lys</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Lysine selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]arg</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Arganine selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]asp</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Aspartic Acid selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]glu</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Glutamic Acid selection, iso charged </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]gln</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Glutamine selection, iso neutral </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>135 </tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0.3 </tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ignh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Ignore hydrogen atoms that are in the <a href="pdb.html">pdb</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]missing</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Continue when atoms are missing, dangerous </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Be slightly more verbose in messages </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-posrefc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>1000 </tt> </TD><TD> Force constant for position restraints </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-vsite</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to virtual sites: <tt>none</tt>, <tt>hydrogens</tt> or <tt>aromatics</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]heavyh</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Make hydrogen atoms heavy </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]deuterate</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change the mass of hydrogens to 2 amu </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">protonated.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">protonated.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
<hr>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Protein unfolding</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Peptide</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
</body>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.1</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
</body>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
-tpbconv can edit run input files in three ways.<p><b>1st.</b> by creating a run input file
+tpbconv can edit run input files in four ways.<p><b>1st.</b> by modifying the number of steps in a run input file
+with option <tt>-nsteps</tt> or option <tt>-runtime</tt>.<p>
+<b>2st.</b> (OBSOLETE) by creating a run input file
for a continuation run when your simulation has crashed due to e.g.
a full disk, or by making a continuation run input file.
-Note that a frame with coordinates and velocities is needed,
-which means that when you never write velocities, you can not use
-tpbconv and you have to start the run again from the beginning.
+This option is obsolete, since <a href="mdrun.html">mdrun</a> now writes and reads
+checkpoint files.
+Note that a frame with coordinates and velocities is needed.
When pressure and/or Nose-Hoover temperature coupling is used
an energy file can be supplied to get an exact continuation
of the original run.<p>
-<b>2nd.</b> by creating a tpx file for a subset of your original
+<b>3nd.</b> by creating a tpx file for a subset of your original
tpx file, which is useful when you want to remove the solvent from
your tpx file, or when you want to make e.g. a pure Ca tpx file.
<b>WARNING: this tpx file is not fully functional</b>.
-<b>3rd.</b> by setting the charges of a specified group
+<b>4rd.</b> by setting the charges of a specified group
to zero. This is useful when doing free energy estimates
-using the LIE (Linear Interactio Energy) method.
+using the LIE (Linear Interaction Energy) method.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Generic energy: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.trr</a></tt> </TD><TD> Input, Opt. </TD><TD> Full precision trajectory: <a href="trr.html">trr</a> <a href="trj.html">trj</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ener.edr</a></tt> </TD><TD> Input, Opt. </TD><TD>
Energy file: <a href="edr.html">edr</a> <a href="ene.html">ene</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> tpxout.tpr</a></tt> </TD><TD> Output </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> tpxout.tpr</a></tt> </TD><TD> Output </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]unconstrained</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> For a continuous trajectory, the constraints should not be solved before the first step (default) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nsteps</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-1</tt> </TD><TD> Change the number of steps </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-runtime</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Set the run time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cont</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> For exact continuation, the constraints should not be solved before the first step </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Mult. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output, Mult. </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input, Mult. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output, Mult. </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-demux</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> remd.xvg</a></tt> </TD><TD> Input, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> First time to use (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Last time to use (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> First time to use (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Last time to use (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Read and write velocities if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Change starting time interactively </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]keeplast</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> keep overlapping frames at end of trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]cat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> do not discard double time frames </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Change starting time interactively </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]keeplast</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> keep overlapping frames at end of trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> do not discard double time frames </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
trjconv can convert trajectory files in many ways:<br>
<b>1.</b> from one format to another<br>
-<b>2.</b> select a subset of atoms<br><b>3.</b> remove periodicity from molecules<br>
+<b>2.</b> select a subset of atoms<br><b>3.</b> change the periodicity representation<br>
<b>4.</b> keep multimeric molecules together<br>
<b>5.</b> center atoms in the box<br>
<b>6.</b> fit atoms to reference structure<br>
conformational transitions.<p>
Option <tt>-pbc</tt> sets the type of periodic boundary condition
treatment:<br>
-* <tt>whole</tt> puts the atoms in the box and then makes
-broken molecules whole (a run input file is required).
-Atom number 1 of each molecule will be inside the box.<br>
-* <tt>com</tt> puts the center of mass of all <it>residues</it>
-in the box. Not that this can break molecules that consist of
-more than one residue (e.g. proteins).<br>
-* <tt>inbox</tt> puts all the atoms in the box.<br>
+* <tt>mol</tt> puts the center of mass of molecules in the box.<br>
+* <tt>res</tt> puts the center of mass of residues in the box.<br>
+* <tt>atom</tt> puts all the atoms in the box.<br>
* <tt>nojump</tt> checks if atoms jump across the box and then puts
them back. This has the effect that all molecules
will remain whole (provided they were whole in the initial
such that they are all closest to the center of mass of the cluster
which is iteratively updated. Note that this will only give meaningful
results if you in fact have a cluster. Luckily that can be checked
-afterwards using a trajectory viewer.<br>
-<tt>-pbc</tt> is ignored when <tt>-fit</tt> or <tt>-pfit</tt> is set,
-
in that case molecules will be made whole.<p>
+afterwards using a trajectory viewer. Note also that if your molecules
+are broken this will not work either.<br>
+
* <tt>whole</tt> only makes broken molecules whole.<p>
Option <tt>-ur</tt> sets the unit cell representation for options
-<tt>whole</tt> and <tt>inbox</tt> of <tt>-pbc</tt>.
+<tt>mol</tt>, <tt>res</tt> and <tt>atom</tt> of <tt>-pbc</tt>.
All three options give different results for triclinc boxes and
identical results for rectangular boxes.
<tt>rect</tt> is the ordinary brick shape.
<tt>compact</tt> puts all atoms at the closest distance from the center
of the box. This can be useful for visualizing e.g. truncated
octahedrons. The center for options <tt>tric</tt> and <tt>compact</tt>
-is <tt>tric</tt> (see below), unless the option <tt>-center</tt>
+is <tt>tric</tt> (see below), unless the option <tt>-boxcenter</tt>
is set differently.<p>
Option <tt>-center</tt> centers the system in the box. The user can
select the group which is used to determine the geometrical center.
-The center options are:
+Option <tt>-boxcenter</tt> sets the location of the center of the box
+for options <tt>-pbc</tt> and <tt>-center</tt>. The center options are:
<tt>tric</tt>: half of the sum of the box vectors,
<tt>rect</tt>: half of the box diagonal,
<tt>zero</tt>: zero.
-Use option <tt>-pbc whole</tt> in addition to <tt>-center</tt> when you
+Use option <tt>-pbc mol</tt> in addition to <tt>-center</tt> when you
want all molecules in the box after the centering.<p>
With <tt>-dt</tt> it is possible to reduce the number of
frames in the output. This option relies on the accuracy of the times
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output </TD><TD>
Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> trajout.xtc</a></tt> </TD><TD> Output </TD><TD>
Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-fr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> frames.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-sub</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> cluster.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt>, <tt>s</tt>, <tt>m</tt> or <tt>h</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tu</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>ps</tt> </TD><TD> Time unit: <tt>ps</tt>, <tt>fs</tt>, <tt>ns</tt>, <tt>us</tt>, <tt>ms</tt> or <tt>s</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only write every nr-th frame </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</tt> </TD><TD> Dump frame nearest specified time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-t0</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Starting time (ps) (default: don't change) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-timestep</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Change time step between input frames (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-pbc</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> PBC treatment (see help text for full description): <tt>none</tt>, <tt>whole</tt>, <tt>inbox</tt>, <tt>nojump</tt>, <tt>cluster</tt> or <tt>com</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dump</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>-1 </tt> </TD><TD> Dump frame nearest specified time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-t0</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Starting time (ps) (default: don't change) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-timestep</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Change time step between input frames (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-pbc</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> PBC treatment (see help text for full description): <tt>none</tt>, <tt>mol</tt>, <tt>res</tt>, <tt>atom</tt>, <tt>nojump</tt>, <tt>cluster</tt> or <tt>whole</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ur</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rect</tt> </TD><TD> Unit-cell representation: <tt>rect</tt>, <tt>tric</tt> or <tt>compact</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-center</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Center atoms in box: <tt>no</tt>, <tt>tric</tt>, <tt>rect</tt> or <tt>zero</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]center</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Center atoms in box </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-boxcenter</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>tric</tt> </TD><TD> Center for -pbc and -center: <tt>tric</tt>, <tt>rect</tt> or <tt>zero</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-box</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Size for new cubic box (default: read from input) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trans</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> All coordinates will be translated by trans. This can advantageously be combined with -pbc mol -ur compact. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-shift</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> All coordinates will be shifted by framenr*shift </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit molecule to ref structure in the structure file: <tt>none</tt>, <tt>rot+trans</tt>, <tt>translation</tt> or <tt>progressive</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-fit</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit molecule to ref structure in the structure file: <tt>none</tt>, <tt>rot+trans</tt>, <tt>rotxy+transxy</tt>, <tt>translation</tt> or <tt>progressive</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-ndec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Read and write velocities if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]force</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Read and write forces if possible </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-trunc</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>
-1</tt> </TD><TD> Truncate input <a href="trj.html">trj</a> file after this time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Read and write velocities if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]force</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Read and write forces if possible </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-trunc</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>
-1 </tt> </TD><TD> Truncate input <a href="trj.html">trj</a> file after this time (ps) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-exec</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Execute command for every output frame with the frame number as argument </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Append output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-split</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Start writing new file when t MOD split = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use 'TER' in <a href="pdb.html">pdb</a> file as end of frame in stead of default 'ENDMDL' </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dropunder</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Drop all frames below this value </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dropover</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Drop all frames above this value </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Append output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-split</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Start writing new file when t MOD split = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-nzero</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Prepend file number in case you use the -sep flag with this number of zeroes </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ter</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use 'TER' in <a href="pdb.html">pdb</a> file as end of frame in stead of default 'ENDMDL' </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dropunder</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Drop all frames below this value </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dropover</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Drop all frames above this value </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
In that case the reference group would be the protein and the group
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
-with any Gromacs program to analyze the n closest waters.<p>
+with any Gromacs program to analyze the n closest waters.
+<p>
If the output file is a <a href="pdb.html">pdb</a> file, the distance to the reference target
will be stored in the B-factor field in order to color with e.g. rasmol.
+<p>
+With option <tt>-nshell</tt> the number of molecules within a shell
+of radius <tt>-r</tt> around the refernce group are printed.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html"> index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ordered.xtc</a></tt> </TD><TD> Output
</TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> ordered.xtc</a></tt> </TD><TD> Output
, Opt. </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-nshell</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> nshell.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes</tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]xvgr</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
yes </tt> </TD><TD> Add specific codes (legends etc.) in the output <a href="xvg.html">xvg</a> files for the xmgrace program </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-na</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of atoms in a molecule </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-da</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Atom used for the distance calculation </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use the distance to the center of mass of the reference group </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]com</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the distance to the center of mass of the reference group </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<h3>Description</h3>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Water</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>19</tt> </TD><TD> Set the nicelevel </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-r0</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> The first residue number in the sequence </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-rot0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Rotate around an angle initially (90 degrees makes sense) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-rot0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Rotate around an angle initially (90 degrees makes sense) </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-T</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Plot a title in the center of the wheel (must be shorter than 10 characters, or it will overwrite the wheel) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]nn</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Toggle numbers </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]nn</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Toggle numbers </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> conf.gro</a></tt> </TD><TD> Input </TD><TD> Structure file: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="top.html"> out.top</a></tt> </TD><TD> Output, Opt. </TD><TD> Topology file </TD></TR>
<TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="rtp.html"> out.rtp</a></tt> </TD><TD> Output, Opt. </TD><TD> Residue Type file used by <a href="pdb2gmx.html">pdb2gmx</a> </TD></TR>
</TABLE>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 1.1</tt> </TD><TD> Scaling factor for bonds with unknown atom types relative to atom type O </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>select</tt> </TD><TD> Select the force field for your simulation. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ff</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>oplsaa</tt> </TD><TD> Force field for your simulation. Type "select" for interactive selcection. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate verbose output in the <a href="top.html">top</a> file. </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nexcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of exclusions </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Generate all proper dihedrals </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]remdih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Remove dihedrals on the same bond as an improper </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Generate all proper dihedrals </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]remdih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Remove dihedrals on the same bond as an improper </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-name</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>ICE</tt> </TD><TD> Name of your molecule </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Use periodic boundary conditions. </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print parameters in the output </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Round off measured values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Use periodic boundary conditions. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pdbq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Use the B-factor supplied in a <a href="pdb.html">pdb</a> file for the atomic charges </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Print parameters in the output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Round off measured values </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 400</tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 5</tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400 </tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>5 </tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
</TABLE>
<P>
+<H3>Known problems</H3>
<UL>
<LI>The atom type selection is primitive. Virtually no chemical knowledge is used
<LI>Periodic boundary conditions screw up the bonding
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
half of the second one (<tt>-f2</tt>). The diagonal will contain
values from the matrix file selected with <tt>-diag</tt>.
Plotting of the diagonal values can be suppressed altogether by
-setting <tt>-diag</tt> to <tt>none</tt>. With
-<tt>-combine</tt> an alternative operation can be selected to combine
-the matrices. In this case, a new color map will be generated with
-a red gradient for negative numbers and a blue for positive.<p>
+setting <tt>-diag</tt> to <tt>none</tt>.
+In this case, a new color <a href="map.html">map</a> will be generated with
+a red gradient for negative numbers and a blue for positive.
If the color coding and legend labels of both matrices are identical,
only one legend will be displayed, else two separate legends are
-displayed.<p>
+displayed.
+With <tt>-combine</tt> an alternative operation can be selected
+to combine the matrices. The output range is automatically set
+to the actual range of the combined matrix. This can be overridden
+with <tt>-cmin</tt> and <tt>-cmax</tt>.<p>
<tt>-title</tt> can be set to <tt>none</tt> to suppress the title, or to
<tt>ylabel</tt> to show the title in the Y-label position (alongside
the Y-axis).<p>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]frame</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Display frame, ticks, labels, title and legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]w</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> View output <a href="xvg.html">xvg</a>, <a href="xpm.html">xpm</a>, <a href="eps.html">eps</a> and <a href="pdb.html">pdb</a> files </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]frame</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>yes </tt> </TD><TD> Display frame, ticks, labels, title and legend </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-title</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>top</tt> </TD><TD> Show title at: <tt><a href="top.html">top</a></tt>, <tt>once</tt>, <tt>ylabel</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]yonce</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Show y-label only once </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]yonce</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Show y-label only once </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-legend</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>both</tt> </TD><TD> Show legend: <tt>both</tt>, <tt>first</tt>, <tt>second</tt> or <tt>none</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-diag</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>first</tt> </TD><TD> Diagonal: <tt>first</tt>, <tt>second</tt> or <tt>none</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-combine</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>halves</tt> </TD><TD> Combine two matrices: <tt>halves</tt>, <tt>add</tt>, <tt>sub</tt>, <tt>mult</tt> or <tt>div</tt> </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-size</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 400</tt> </TD><TD> Horizontal size of the matrix in ps units </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Element x-size, overrides -size (also y-size when -by is not set) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-by</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Element y-size </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-size</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400 </tt> </TD><TD> Horizontal size of the matrix in ps units </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Element x-size, overrides -size (also y-size when -by is not set) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-by</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Element y-size </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-rainbow</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Rainbow colors, convert white to: <tt>no</tt>, <tt>blue</tt> or <tt>red</tt> </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-gradient</tt></b> </TD><TD ALIGN=RIGHT> vector </TD><TD ALIGN=RIGHT> <tt>0 0 0</tt> </TD><TD> Re-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b} </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> only write out every nr-th row and column </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroline</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no</tt> </TD><TD> insert line in <a href="xpm.html">xpm</a> matrix where axis label is zero </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroline</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>
no </tt> </TD><TD> insert line in <a href="xpm.html">xpm</a> matrix where axis label is zero </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-legoffset</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Skip first N colors from <a href="xpm.html">xpm</a> file for the legend </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-combine</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>halves</tt> </TD><TD> Combine two matrices: <tt>halves</tt>, <tt>add</tt>, <tt>sub</tt>, <tt>mult</tt> or <tt>div</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cmin</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Minimum for combination output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-cmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Maximum for combination output </TD></TD>
</TABLE>
<P>
<hr>
<TR><TD WIDTH=400>
<TABLE WIDTH=400 NOBORDER>
<TD WIDTH=116>
-<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
+<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.png"BORDER=0 </a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.3_beta_20050823<br>
-Mon 29 Aug 2005</B></td></tr></TABLE>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0_rc1<br>
+Mon 22 Sep 2008</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
<p>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> xml </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> traj.xtc</a></tt> </TD><TD> Input </TD><TD> Trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> cpt </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html"> topol.tpr</a></tt> </TD><TD> Input </TD><TD> Run input file: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<TR><TH>option</TH><TH>type</TH><TH>default</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Print help info and quit </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]h</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>no </tt> </TD><TD> Print help info and quit </TD></TD>
<TR><TD ALIGN=RIGHT> <b><tt>-nice</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Set the nicelevel </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> First frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Last frame (ps) to read from trajectory </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>0 </tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
<hr>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<CENTER><TABLE BORDER=0 CELLSPACING=0 CELLPADDING=0 COLS=2 WIDTH="98%">
<TR>
<TD><font size=-1><A HREF="../online.html">Main Table of Contents</A></font></TD>
-<TD ALIGN=RIGHT><B>VERSION 3.2</B></TR>
+<TD ALIGN=RIGHT><B>VERSION 4.0</B></TR>
<TR><TD><font size=-1><A HREF="http://www.gromacs.org">GROMACS homepage</A></font></TD>
<TD ALIGN=RIGHT><B>Sun 25 Jan 2004</B></TR></TABLE></CENTER><HR>
<H3>Description</H3>
<a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>Getting started - Your Own</h2>
<font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.2<br>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 4.0<br>
Sun 25 Jan 2004</B></td></tr></TABLE>
<HR>
LIBS = -lmd@LIBSUFFIX@ -lgmx@LIBSUFFIX@ @LIBS@
CC = @CC@
if GMX_DOUBLE
-MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@ -DGMX_DOUBLE
+MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@ -I@includedir@/gromacs -DGMX_DOUBLE
else
-MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@
+MYCFLAGS = @CFLAGS@ @INCLUDES@ -I@includedir@ -I@includedir@/gromacs
endif
if GMX_DOUBLE
-6
+7
CYS SG 1 CYS SG 1 0.2 CYS2 CYS2
CYS SG 1 HEME FE 2 0.25 CYS2 HEME
CYS SG 1 HEME CAB 1 0.18 CYS2 HEME
CYS SG 1 HEME CAC 1 0.18 CYS2 HEME
HIS NE2 1 HEME FE 1 0.2 HIS1 HEME
MET SD 1 HEME FE 1 0.24 MET HEME
+CYM SG 1 CYM SG 1 0.2 CYS2 CYS2
FILE *in;
char buf[256];
gmx_mtop_t *mtop;
+ t_topology top;
t_trxframe fr;
int i,ftp,natoms,i1;
real d,r1,r2;
*ePBC = i;
strcpy(title,*(mtop->name));
-
+
/* Free possibly allocated memory */
done_atom(atoms);
*atoms = gmx_mtop_global_atoms(mtop);
-
+ top = gmx_mtop_t_to_t_topology(mtop);
+ tpx_make_chain_identifiers(atoms,&top.mols);
+
done_mtop(mtop,FALSE);
sfree(mtop);
-
+ done_top(&top);
+
break;
default:
gmx_incons("Not supported in read_stx_conf");
snrm2.c sscal.c ssymv.c ssyr2k.c \
strmv.c isamax.c
+EXTRA_DIST = blas_copyright
+
CLEANFILES = *.la *~ \\\#*
--- /dev/null
+These files are semi-automatic translations by f2c from the original netlib BLAS library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and
+not the reference BLAS implementation.
+
+The reference BLAS implementation is available from http://www.netlib.org/blas
+
+BLAS does not come with a formal named "license", but a general statement that
+
+"The reference BLAS is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+our modified BLAS files as the original netlib versions, so do what you want with them.
+However, be warned that we have only tested that they to the right thing in the cases used
+in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
+
slarrvx.c \
ilasrt2.c lapack_limits.h
+EXTRA_DIST = lapack_copyright
CLEANFILES = *.la *~ \\\#*
--- /dev/null
+These files are semi-automatic translations by f2c from the original netlib LAPACK library.
+The source has been modified to (mostly) use modern C formatting, and to get rid of
+compiler warnings. Any errors in doing this should be blamed on the Gromacs developers, and
+not the reference LAPACK implementation.
+
+The reference LAPACK implementation is available from http://www.netlib.org/lapack
+
+LAPACK does not come with a formal named "license", but a general statement saying:
+
+"The reference LAPACK is a freely-available software package. It is available from netlib
+via anonymous ftp and the World Wide Web. Thus, it can be included in commercial software
+packages (and has been). We only ask that proper credit be given to the authors."
+
+While the rest of Gromacs is GPL, we think it's only fair to give you the same rights to
+our modified LAPACK files as the original netlib versions, so do what you want with them.
+
+However, be warned that we have only tested that they to the right thing in the cases used
+in Gromacs (primarily full & sparse matrix diagonalization), so in most cases it is a much
+better idea to use the full reference implementation.
+
+Erik Lindahl, 2008-10-07.
+
F77_FUNC(xdrfbool,XDRFBOOL)(int *xdrid, int *pb, int *ret)
{
*ret = xdr_bool(xdridptr[*xdrid], pb);
- cnt += sizeof(int);
+ cnt += XDR_INT_SIZE;
}
void
F77_FUNC(xdrfint,XDRFINT)(int *xdrid, int *ip, int *ret)
{
*ret = xdr_int(xdridptr[*xdrid], ip);
- cnt += sizeof(int);
+ cnt += XDR_INT_SIZE;
}
F77_FUNC(xdrfshort,XDRFSHORT)(int *xdrid, short *sp, int *ret)
static const int header_size = 16;
+/* This is just for clarity - it can never be anything but 4! */
+#define XDR_INT_SIZE 4
/* Check if we are at the header start.
At the same time it will also read 1 int */
/* read magic natoms and timestep */
for(i = 0;i<3;i++){
if(!xdr_int(xdrs, &(i_inp[i]))){
- gmx_fseek(fp,off+sizeof(int),SEEK_SET);
+ gmx_fseek(fp,off+XDR_INT_SIZE,SEEK_SET);
return -1;
}
}
/* quick return */
if(i_inp[0] != XTC_MAGIC){
- if(gmx_fseek(fp,off+sizeof(int),SEEK_SET)){
+ if(gmx_fseek(fp,off+XDR_INT_SIZE,SEEK_SET)){
return -1;
}
return 0;
/* read time and box */
for(i = 0;i<10;i++){
if(!xdr_float(xdrs, &(f_inp[i]))){
- gmx_fseek(fp,off+sizeof(int),SEEK_SET);
+ gmx_fseek(fp,off+XDR_INT_SIZE,SEEK_SET);
return -1;
}
}
if(i_inp[1] == natoms &&
((f_inp[1] != 0 && f_inp[6] == 0) ||
(f_inp[1] == 0 && f_inp[5] == 0 && f_inp[9] == 0))){
- if(gmx_fseek(fp,off+sizeof(int),SEEK_SET)){
+ if(gmx_fseek(fp,off+XDR_INT_SIZE,SEEK_SET)){
return -1;
}
*time = f_inp[0];
*timestep = i_inp[2];
return 1;
}
- if(gmx_fseek(fp,off+sizeof(int),SEEK_SET)){
+ if(gmx_fseek(fp,off+XDR_INT_SIZE,SEEK_SET)){
return -1;
}
return 0;
return -1;
}else if(ret == 0){
/*Go back.*/
- if(gmx_fseek(fp,-8,SEEK_CUR)){
+ if(gmx_fseek(fp,-2*XDR_INT_SIZE,SEEK_CUR)){
return -1;
}
}
if(ret == 1){
*bOK = 1;
if(gmx_fseek(fp,off,SEEK_SET)){
+ *bOK = 0;
return -1;
}
return step;
return -1;
}
return -1;
+
+ }else if(ret == 0){
+ /*Go back.*/
+ if(gmx_fseek(fp,-2*XDR_INT_SIZE,SEEK_CUR)){
+ return -1;
+ }
}
}
return -1;
ret = xtc_at_header_start(fp,xdrs,natoms,&step,&time);
if(ret == 1){
if((res = gmx_ftell(fp)) >= 0){
- return res - sizeof(int);
+ return res - XDR_INT_SIZE;
}else{
return res;
}
}
/* round to 4 bytes */
- high /= sizeof(int);
- high *= sizeof(int);
- offset = ((high/2)/sizeof(int))*sizeof(int);
+ high /= XDR_INT_SIZE;
+ high *= XDR_INT_SIZE;
+ offset = ((high/2)/XDR_INT_SIZE)*XDR_INT_SIZE;
if(gmx_fseek(fp,offset,SEEK_SET)){
return -1;
return -1;
}
/* round to int */
- high /= sizeof(int);
- high *= sizeof(int);
- offset = ((high/2)/sizeof(int))*sizeof(int);
+ high /= XDR_INT_SIZE;
+ high *= XDR_INT_SIZE;
+ offset = ((high/2)/XDR_INT_SIZE)*XDR_INT_SIZE;
if(gmx_fseek(fp,offset,SEEK_SET)){
return -1;
return -1;
}
/* round to 4 bytes and subtract header*/
- offset = (((high+low)/2)/sizeof(int))*sizeof(int);
+ offset = (((high+low)/2)/XDR_INT_SIZE)*XDR_INT_SIZE;
if(gmx_fseek(fp,offset,SEEK_SET)){
return -1;
}
return -1;
}
- if( (res = gmx_fseek(fp,-4,SEEK_END)) != 0){
+ if( (res = gmx_fseek(fp,-3*XDR_INT_SIZE,SEEK_END)) != 0){
*bOK = 0;
return -1;
}
}
- if(gmx_fseek(fp,-4,SEEK_END)){
+ if(gmx_fseek(fp,-3*XDR_INT_SIZE,SEEK_END)){
*bOK = 0;
return -1;
}
#include "typedefs.h"
#include "mtop_util.h"
#include "topsort.h"
+#include "symtab.h"
int ncg_mtop(const gmx_mtop_t *mtop)
{
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _nb_free_energy_h_
#define _nb_free_energy_h_
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _nb_generic_h_
#define _nb_generic_h_
if (mknb_fortran) {
mknb_assign (rinv,"frsqrte(dble(%s))",rsq);
} else {
- mknb_assign (rinv,"__frsqrte(dble(%s))",rsq);
+ mknb_assign (rinv,"__frsqrte(double(%s))",rsq);
}
}
mknb_assign(rinv,"(0.5*%s*(3.0-((%s*%s)*%s)))",rinv,rsq,rinv,rinv);
nflops += 5; /* 4 mult and one sub on the last line */
- if(mknb_options.ppc_invsqrt=2)
+ if(mknb_options.ppc_invsqrt==2)
{
/* Older powerpc architectures need two iterations for single, 3 for double */
mknb_assign(rinv,"(0.5*%s*(3.0-((%s*%s)*%s)))",rinv,rsq,rinv,rinv);
/*
* $Id$
- *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
/* IA64 provides 4 different CPUID registers,
/*
* $Id$
- *
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
*/
/* IA64 provides 4 different CPUID registers,
bTER=bSet;
}
-static void gromacs_name(char *name)
+static void xlate_atomname_pdb2gmx(char *name)
{
int i,length;
char temp;
length=strlen(name);
- if (isdigit(name[0])) {
+ if (length>3 && isdigit(name[0])) {
temp=name[0];
for(i=1; i<length; i++)
name[i-1]=name[i];
}
}
+static void xlate_atomname_gmx2pdb(char *name)
+{
+ int i,length;
+ char temp;
+
+ length=strlen(name);
+ if (length>3 && isdigit(name[length-1])) {
+ temp=name[length-1];
+ for(i=length-1; i>0; --i)
+ name[i]=name[i-1];
+ name[0]=temp;
+ }
+}
+
+
void gmx_write_pdb_box(FILE *out,int ePBC,matrix box)
{
real alpha,beta,gamma;
resnr=atoms->atom[i].resnr;
strcpy(resnm,*atoms->resname[resnr]);
strcpy(nm,*atoms->atomname[i]);
+ /* rename HG12 to 2HG1, etc. */
+ xlate_atomname_gmx2pdb(nm);
resnr++;
if (resnr>=10000)
resnr = resnr % 10000;
else
newres=atoms->atom[natom-1].resnr;
if (bChange)
- gromacs_name(anm);
+ xlate_atomname_pdb2gmx(anm);
atoms->atomname[natom]=put_symtab(symtab,anm);
atomn->chain=chain[0];
atomn->resnr=newres;
/* -*- mode: c; tab-width: 4; indent-tabs-mode: nil; c-basic-offset: 4; c-file-style: "stroustrup"; -*- */
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
}
}
-static void make_chain_identifiers(t_atoms *atoms,t_block *mols)
+void
+tpx_make_chain_identifiers(t_atoms *atoms,t_block *mols)
{
int m,a,a0,a1;
char c,chain;
*top = gmx_mtop_t_to_t_topology(mtop);
sfree(mtop);
strcpy(title,*top->name);
- make_chain_identifiers(&top->atoms,&top->mols);
+ tpx_make_chain_identifiers(&top->atoms,&top->mols);
}
else {
get_stx_coordnum(infile,&natoms);
real old[MAXFORCEPARAM],int comb,real reppow)
{
int i,j;
+ real tmp;
/* Set to zero */
for(j=0; (j<MAXFORCEPARAM); j++)
case F_ANGRESZ:
new->pdihs.phiA = old[0];
new->pdihs.cpA = old[1];
- new->pdihs.mult = round_check(old[2],1,ftype,"multiplicity");
+
+ /* Dont do any checks if all parameters are zero (such interactions will be removed) */
+ tmp=fabs(old[0])+fabs(old[1])+fabs(old[2])+fabs(old[3])+fabs(old[4]);
+ new->pdihs.mult = (tmp < GMX_REAL_MIN) ? 0 : round_check(old[2],1,ftype,"multiplicity");
+
new->pdihs.phiB = old[3];
new->pdihs.cpB = old[4];
break;
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
typedef struct gmx_cpp *gmx_cpp_t;
/* The possible return codes for these functions */
/* Check for disulphides and other special bonds */
rename_pdbres(pdba,"CYSH","CYS",TRUE,&symtab);
+ rename_pdbres(pdba,"CYN","CYM",TRUE,&symtab); /* amber */
nssbonds=mk_specbonds(pdba,x,bCysMan,&ssbonds);
rename_pdbres(pdba,"CYS","CYSH",TRUE,&symtab);
-
+ rename_pdbres(pdba,"CYM","CYN",TRUE,&symtab); /* amber */
+
if (debug) {
if ( cc->chain == '\0' || cc->chain == ' ')
sprintf(fn,"chain.pdb");
#include <mkl_dfti.h>
+
#include "gmx_fft.h"
#include "gmx_fatal.h"
+/* For MKL version (<10.0), we should define MKL_LONG. */
+#ifndef MKL_LONG
+#define MKL_LONG long int
+#endif
+
+
#ifdef GMX_DOUBLE
#define GMX_DFTI_PREC DFTI_DOUBLE
#else
};
+
int
gmx_fft_init_1d(gmx_fft_t * pfft,
int nx,
fft->ooplace[3] = NULL;
- status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if( status == 0 )
status = DftiSetValue(fft->inplace[0],DFTI_PLACEMENT,DFTI_INPLACE);
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if( status == 0)
DftiSetValue(fft->ooplace[0],DFTI_PLACEMENT,DFTI_NOT_INPLACE);
}
fft->ooplace[3] = NULL;
- status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_REAL,1,nx);
+ status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)nx);
if( status == 0 )
status = DftiSetValue(fft->inplace[0],DFTI_PLACEMENT,DFTI_INPLACE);
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_REAL,1,nx);
+ status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)nx);
if( status == 0 )
status = DftiSetValue(fft->ooplace[0],DFTI_PLACEMENT,DFTI_NOT_INPLACE);
gmx_fft_t fft;
int d;
int status;
- int length[2];
+ MKL_LONG length[2];
if(pfft==NULL)
{
gmx_fft_t fft;
int d;
int status;
- int stride[2];
- int nyc;
+ MKL_LONG stride[2];
+ MKL_LONG nyc;
if(pfft==NULL)
{
*/
/* In-place X FFT */
- status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if ( status == 0 )
{
/* Out-of-place X FFT */
if( status == 0 )
- status = DftiCreateDescriptor(&(fft->ooplace[0]),GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&(fft->ooplace[0]),GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if( status == 0 )
{
/* In-place Y FFT */
if( status == 0 )
- status = DftiCreateDescriptor(&fft->inplace[1],GMX_DFTI_PREC,DFTI_REAL,1,ny);
+ status = DftiCreateDescriptor(&fft->inplace[1],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)ny);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->inplace[1],DFTI_PLACEMENT,DFTI_INPLACE) ||
- DftiSetValue(fft->inplace[1],DFTI_NUMBER_OF_TRANSFORMS,nx) ||
- DftiSetValue(fft->inplace[1],DFTI_INPUT_DISTANCE,2*nyc) ||
- DftiSetValue(fft->inplace[1],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->inplace[1],DFTI_OUTPUT_DISTANCE,2*nyc) ||
- DftiSetValue(fft->inplace[1],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->inplace[1],DFTI_PLACEMENT,DFTI_INPLACE) ||
+ DftiSetValue(fft->inplace[1],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx) ||
+ DftiSetValue(fft->inplace[1],DFTI_INPUT_DISTANCE,2*nyc) ||
+ DftiSetValue(fft->inplace[1],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->inplace[1],DFTI_OUTPUT_DISTANCE,2*nyc) ||
+ DftiSetValue(fft->inplace[1],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->inplace[1]));
}
/* Out-of-place real-to-complex (affects output distance) Y FFT */
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[1],GMX_DFTI_PREC,DFTI_REAL,1,ny);
+ status = DftiCreateDescriptor(&fft->ooplace[1],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)ny);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->ooplace[1],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[1],DFTI_NUMBER_OF_TRANSFORMS,nx) ||
- DftiSetValue(fft->ooplace[1],DFTI_INPUT_DISTANCE,ny) ||
- DftiSetValue(fft->ooplace[1],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_DISTANCE,2*nyc) ||
- DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[1],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[1],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx) ||
+ DftiSetValue(fft->ooplace[1],DFTI_INPUT_DISTANCE,(MKL_LONG)ny) ||
+ DftiSetValue(fft->ooplace[1],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_DISTANCE,2*nyc) ||
+ DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[1]));
}
/* Out-of-place complex-to-real (affects output distance) Y FFT */
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[2],GMX_DFTI_PREC,DFTI_REAL,1,ny);
+ status = DftiCreateDescriptor(&fft->ooplace[2],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)ny);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->ooplace[2],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[2],DFTI_NUMBER_OF_TRANSFORMS,nx) ||
- DftiSetValue(fft->ooplace[2],DFTI_INPUT_DISTANCE,2*nyc) ||
- DftiSetValue(fft->ooplace[2],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_DISTANCE,ny) ||
- DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[2],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[2],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx) ||
+ DftiSetValue(fft->ooplace[2],DFTI_INPUT_DISTANCE,2*nyc) ||
+ DftiSetValue(fft->ooplace[2],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_DISTANCE,(MKL_LONG)ny) ||
+ DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[2]));
}
{
gmx_fft_t fft;
int d;
- int length[3];
+ MKL_LONG length[3];
int status;
if(pfft==NULL)
length[1] = ny;
length[2] = nz;
- status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,3,length);
+ status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,(MKL_LONG)3,length);
if( status == 0 )
status = DftiSetValue(fft->inplace[0],DFTI_PLACEMENT,DFTI_INPLACE);
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,3,length);
+ status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,(MKL_LONG)3,length);
if( status == 0 )
status = DftiSetValue(fft->ooplace[0],DFTI_PLACEMENT,DFTI_NOT_INPLACE);
gmx_fft_t fft;
int d;
int status;
- int stride[2];
+ MKL_LONG stride[2];
int nzc;
if(pfft==NULL)
* transform distance: 1
* element strides: ny*nzc
*/
- status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&fft->inplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if ( status == 0)
{
stride[1] = ny*nzc;
status =
- (DftiSetValue(fft->inplace[0],DFTI_PLACEMENT,DFTI_INPLACE) ||
- DftiSetValue(fft->inplace[0],DFTI_NUMBER_OF_TRANSFORMS,ny*nzc) ||
- DftiSetValue(fft->inplace[0],DFTI_INPUT_DISTANCE,1) ||
- DftiSetValue(fft->inplace[0],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->inplace[0],DFTI_OUTPUT_DISTANCE,1) ||
- DftiSetValue(fft->inplace[0],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->inplace[0],DFTI_PLACEMENT,DFTI_INPLACE) ||
+ DftiSetValue(fft->inplace[0],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)ny*nzc) ||
+ DftiSetValue(fft->inplace[0],DFTI_INPUT_DISTANCE,1) ||
+ DftiSetValue(fft->inplace[0],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->inplace[0],DFTI_OUTPUT_DISTANCE,1) ||
+ DftiSetValue(fft->inplace[0],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->inplace[0]));
}
* element strides: ny*nzc
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,nx);
+ status = DftiCreateDescriptor(&fft->ooplace[0],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)nx);
if( status == 0 )
{
stride[1] = ny*nzc;
status =
- (DftiSetValue(fft->ooplace[0],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[0],DFTI_NUMBER_OF_TRANSFORMS,ny*nzc) ||
- DftiSetValue(fft->ooplace[0],DFTI_INPUT_DISTANCE,1) ||
- DftiSetValue(fft->ooplace[0],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[0],DFTI_OUTPUT_DISTANCE,1) ||
- DftiSetValue(fft->ooplace[0],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[0],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[0],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)ny*nzc) ||
+ DftiSetValue(fft->ooplace[0],DFTI_INPUT_DISTANCE,1) ||
+ DftiSetValue(fft->ooplace[0],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[0],DFTI_OUTPUT_DISTANCE,1) ||
+ DftiSetValue(fft->ooplace[0],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[0]));
}
* element strides: nzc
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->inplace[1],GMX_DFTI_PREC,DFTI_COMPLEX,1,ny);
+ status = DftiCreateDescriptor(&fft->inplace[1],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)ny);
if( status == 0 )
{
stride[1] = nzc;
status =
- (DftiSetValue(fft->inplace[1],DFTI_PLACEMENT,DFTI_INPLACE) ||
- DftiSetValue(fft->inplace[1],DFTI_NUMBER_OF_TRANSFORMS,nzc) ||
- DftiSetValue(fft->inplace[1],DFTI_INPUT_DISTANCE,1) ||
- DftiSetValue(fft->inplace[1],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->inplace[1],DFTI_OUTPUT_DISTANCE,1) ||
- DftiSetValue(fft->inplace[1],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->inplace[1],DFTI_PLACEMENT,DFTI_INPLACE) ||
+ DftiSetValue(fft->inplace[1],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nzc) ||
+ DftiSetValue(fft->inplace[1],DFTI_INPUT_DISTANCE,1) ||
+ DftiSetValue(fft->inplace[1],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->inplace[1],DFTI_OUTPUT_DISTANCE,1) ||
+ DftiSetValue(fft->inplace[1],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->inplace[1]));
}
* element strides: nzc
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[1],GMX_DFTI_PREC,DFTI_COMPLEX,1,ny);
+ status = DftiCreateDescriptor(&fft->ooplace[1],GMX_DFTI_PREC,DFTI_COMPLEX,1,(MKL_LONG)ny);
if( status == 0 )
{
stride[1] = nzc;
status =
- (DftiSetValue(fft->ooplace[1],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[1],DFTI_NUMBER_OF_TRANSFORMS,nzc) ||
- DftiSetValue(fft->ooplace[1],DFTI_INPUT_DISTANCE,1) ||
- DftiSetValue(fft->ooplace[1],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_DISTANCE,1) ||
- DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[1],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[1],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nzc) ||
+ DftiSetValue(fft->ooplace[1],DFTI_INPUT_DISTANCE,1) ||
+ DftiSetValue(fft->ooplace[1],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_DISTANCE,1) ||
+ DftiSetValue(fft->ooplace[1],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[1]));
}
* element strides: 1
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->inplace[2],GMX_DFTI_PREC,DFTI_REAL,1,nz);
+ status = DftiCreateDescriptor(&fft->inplace[2],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)nz);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->inplace[2],DFTI_PLACEMENT,DFTI_INPLACE) ||
- DftiSetValue(fft->inplace[2],DFTI_NUMBER_OF_TRANSFORMS,nx*ny) ||
- DftiSetValue(fft->inplace[2],DFTI_INPUT_DISTANCE,nzc*2) ||
- DftiSetValue(fft->inplace[2],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->inplace[2],DFTI_OUTPUT_DISTANCE,nzc*2) ||
- DftiSetValue(fft->inplace[2],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->inplace[2],DFTI_PLACEMENT,DFTI_INPLACE) ||
+ DftiSetValue(fft->inplace[2],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx*ny) ||
+ DftiSetValue(fft->inplace[2],DFTI_INPUT_DISTANCE,(MKL_LONG)nzc*2) ||
+ DftiSetValue(fft->inplace[2],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->inplace[2],DFTI_OUTPUT_DISTANCE,(MKL_LONG)nzc*2) ||
+ DftiSetValue(fft->inplace[2],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->inplace[2]));
}
* element STRIDES: 1
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[2],GMX_DFTI_PREC,DFTI_REAL,1,nz);
+ status = DftiCreateDescriptor(&fft->ooplace[2],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)nz);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->ooplace[2],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[2],DFTI_NUMBER_OF_TRANSFORMS,nx*ny) ||
- DftiSetValue(fft->ooplace[2],DFTI_INPUT_DISTANCE,nz) ||
- DftiSetValue(fft->ooplace[2],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_DISTANCE,nzc*2) ||
- DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[2],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[2],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx*ny) ||
+ DftiSetValue(fft->ooplace[2],DFTI_INPUT_DISTANCE,(MKL_LONG)nz) ||
+ DftiSetValue(fft->ooplace[2],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_DISTANCE,(MKL_LONG)nzc*2) ||
+ DftiSetValue(fft->ooplace[2],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[2]));
}
* element STRIDES: 1
*/
if( status == 0 )
- status = DftiCreateDescriptor(&fft->ooplace[3],GMX_DFTI_PREC,DFTI_REAL,1,nz);
+ status = DftiCreateDescriptor(&fft->ooplace[3],GMX_DFTI_PREC,DFTI_REAL,1,(MKL_LONG)nz);
if( status == 0 )
{
stride[1] = 1;
status =
- (DftiSetValue(fft->ooplace[3],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
- DftiSetValue(fft->ooplace[3],DFTI_NUMBER_OF_TRANSFORMS,nx*ny) ||
- DftiSetValue(fft->ooplace[3],DFTI_INPUT_DISTANCE,nzc*2) ||
- DftiSetValue(fft->ooplace[3],DFTI_INPUT_STRIDES,stride) ||
- DftiSetValue(fft->ooplace[3],DFTI_OUTPUT_DISTANCE,nz) ||
- DftiSetValue(fft->ooplace[3],DFTI_OUTPUT_STRIDES,stride) ||
+ (DftiSetValue(fft->ooplace[3],DFTI_PLACEMENT,DFTI_NOT_INPLACE) ||
+ DftiSetValue(fft->ooplace[3],DFTI_NUMBER_OF_TRANSFORMS,(MKL_LONG)nx*ny) ||
+ DftiSetValue(fft->ooplace[3],DFTI_INPUT_DISTANCE,(MKL_LONG)nzc*2) ||
+ DftiSetValue(fft->ooplace[3],DFTI_INPUT_STRIDES,stride) ||
+ DftiSetValue(fft->ooplace[3],DFTI_OUTPUT_DISTANCE,(MKL_LONG)nz) ||
+ DftiSetValue(fft->ooplace[3],DFTI_OUTPUT_STRIDES,stride) ||
DftiCommitDescriptor(fft->ooplace[3]));
}
}
else
{
- /* real-to-complex in Y dimension, in_data in out_data */
+ /* real-to-complex in Y dimension, in_data to out_data */
status = DftiComputeForward(fft->ooplace[1],in_data,out_data);
- /* complex-to-complex in X dimension, in-place in out_data */
+ /* complex-to-complex in X dimension, in-place to out_data */
if ( status == 0 )
status = DftiComputeForward(fft->inplace[0],out_data);
}
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifdef HAVE_CONFIG_H
#include <config.h>
#endif
+/*
+ * $Id$
+ *
+ * This source code is part of
+ *
+ * G R O M A C S
+ *
+ * GROningen MAchine for Chemical Simulations
+ *
+ * Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
+ * Copyright (c) 1991-2000, University of Groningen, The Netherlands.
+ * Copyright (c) 2001-2008, The GROMACS development team,
+ * check out http://www.gromacs.org for more information.
+
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU General Public License
+ * as published by the Free Software Foundation; either version 2
+ * of the License, or (at your option) any later version.
+ *
+ * If you want to redistribute modifications, please consider that
+ * scientific software is very special. Version control is crucial -
+ * bugs must be traceable. We will be happy to consider code for
+ * inclusion in the official distribution, but derived work must not
+ * be called official GROMACS. Details are found in the README & COPYING
+ * files - if they are missing, get the official version at www.gromacs.org.
+ *
+ * To help us fund GROMACS development, we humbly ask that you cite
+ * the papers on the package - you can find them in the top README file.
+ *
+ * For more info, check our website at http://www.gromacs.org
+ *
+ * And Hey:
+ * Gallium Rubidium Oxygen Manganese Argon Carbon Silicon
+ */
+
#ifndef _correl_h
#define _correl_h
"a specific position (as with position restraints)."
};
static rvec fc={1000.0,1000.0,1000.0};
- static real freeze_level;
+ static real freeze_level = 0.0;
static real disre_dist = 0.1;
static real disre_frac = 0.0;
static real disre_up2 = 1.0;
static bool bDisre=FALSE;
static bool bConstr=FALSE;
+
t_pargs pa[] = {
{ "-fc", FALSE, etRVEC, {fc},
"force constants (kJ mol-1 nm-2)" },
asize(desc),desc,0,NULL);
bFreeze = opt2bSet("-of",NFILE,fnm) || opt2parg_bSet("-freeze",asize(pa),pa);
- bDisre = bDisre || opt2parg_bSet("disre_dist",npargs,pa);
+ bDisre = bDisre || opt2parg_bSet("-disre_dist",npargs,pa);
xfn = opt2fn_null("-f",NFILE,fnm);
nfn = opt2fn_null("-n",NFILE,fnm);
int gmx_principal(int argc,char *argv[])
{
static char *desc[] = {
- "g_principal calculates the three principal axes of inertion for a group",
+ "g_principal calculates the three principal axes of inertia for a group",
"of atoms.",
};
+ static bool foo = FALSE;
t_pargs pa[] = {
+ { "-foo", FALSE, etBOOL, {&foo}, "Dummy option to avoid empty array" }
};
int status;
t_topology top;
pdbatoms->pdbinfo[aid].uij[U13] = 1e6*U[i][XX*DIM + ZZ];
pdbatoms->pdbinfo[aid].uij[U23] = 1e6*U[i][YY*DIM + ZZ];
}
- sfree(U);
}
if (bRes) {
average_residues(rmsf,isize,index,w_rls,&top.atoms);
print_dir(fp,Uaver);
fclose(fp);
}
-
+
+ for(i=0; i<isize; i++)
+ sfree(U[i]);
+ sfree(U);
+
/* Write RMSF output */
if (bReadPDB) {
bfac = 8.0*M_PI*M_PI/3.0*100;
}
void sas_plot(int nfile,t_filenm fnm[],real solsize,int ndots,
- real qcut,bool bSave,real minarea,
+ real qcut,bool bSave,real minarea,bool bPBC,
real dgs_default,bool bFindex)
{
FILE *fp,*fp2,*fp3=NULL,*vp;
&t,&x,box))==0)
gmx_fatal(FARGS,"Could not read coordinates from statusfile\n");
+ if ((ePBC != epbcXYZ) || (TRICLINIC(box))) {
+ fprintf(stderr,"\n\nWARNING: non-rectangular boxes may give erroneous results or crashes.\n"
+ "Analysis based on vacuum simulations (with the possibility of evaporation)\n"
+ "will certainly crash the analysis.\n\n");
+ }
+
snew(nx,2);
snew(index,2);
snew(grpname,2);
nfr=0;
do {
- rm_pbc(&top->idef,ePBC,natoms,box,x,x);
+ if (bPBC)
+ rm_pbc(&top->idef,ePBC,natoms,box,x,x);
bConnelly = (nfr==0 && opt2bSet("-q",nfile,fnm));
if (bConnelly)
retval = nsc_dclm_pbc(x,radius,nx[0],ndots,flag,&totarea,
&area,&totvolume,&surfacedots,&nsurfacedots,
- index[0],ePBC,box);
+ index[0],ePBC,bPBC ? box : NULL);
if (retval)
gmx_fatal(FARGS,"Something wrong in nsc_dclm2");
"generated (option [TT]-i[tt])",
"which can be used to restrain surface atoms.[PAR]",
"By default, periodic boundary conditions are taken into account,",
- "this can be turned off using the [TT]-pbc[tt] option.[PAR]",
+ "this can be turned off using the [TT]-nopbc[tt] option.[PAR]",
"With the [TT]-tv[tt] option the total volume and density of the molecule can be",
"computed.",
"Please consider whether the normal probe radius is appropriate",
static int ndots = 24;
static real qcut = 0.2;
static real minarea = 0.5, dgs_default=0;
- static bool bSave = TRUE,bFindex=FALSE;
+ static bool bSave = TRUE,bPBC=TRUE,bFindex=FALSE;
t_pargs pa[] = {
{ "-probe", FALSE, etREAL, {&solsize},
"Radius of the solvent probe (nm)" },
"Determine from a group in the index file what are the hydrophobic atoms rather than from the charge" },
{ "-minarea", FALSE, etREAL, {&minarea},
"The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file (see help)" },
+ { "-pbc", FALSE, etBOOL, {&bPBC},
+ "Take periodicity into account" },
{ "-prot", FALSE, etBOOL, {&bSave},
"Output the protein to the connelly pdb file too" },
{ "-dgs", FALSE, etREAL, {&dgs_default},
please_cite(stderr,"Eisenhaber95");
- sas_plot(NFILE,fnm,solsize,ndots,qcut,bSave,minarea,dgs_default,bFindex);
+ sas_plot(NFILE,fnm,solsize,ndots,qcut,bSave,minarea,bPBC,dgs_default,bFindex);
do_view(opt2fn("-o",NFILE,fnm),"-nxy");
do_view(opt2fn_null("-or",NFILE,fnm),"-nxy");
#define UNSP_ICO_DOD 9
#define UNSP_ICO_ARC 10
-typedef real * point_real;
-typedef int * point_int;
-point_real xpunsp=NULL;
-real del_cube;
-point_int ico_wk=NULL, ico_pt=NULL;
-int n_dot, ico_cube, last_n_dot=0, last_densit=0, last_unsp=0;
-int last_cubus=0;
+real *xpunsp=NULL;
+real del_cube;
+int *ico_wk=NULL, *ico_pt=NULL;
+int n_dot, ico_cube, last_n_dot=0, last_densit=0, last_unsp=0;
+int last_cubus=0;
#define FOURPI (4.*M_PI)
#define TORAD(A) ((A)*0.017453293)
real a, d, x, y, z, x2, y2, z2, x3, y3, z3;
real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
xjk, yjk, zjk, xkj, ykj, zkj;
- point_real xus=NULL;
+ real *xus=NULL;
/* calculate tessalation level */
a = sqrt((((real) densit)-2.)/10.);
real a, d, x, y, z, x2, y2, z2, x3, y3, z3, ai_d, adod;
real xij, yij, zij, xji, yji, zji, xik, yik, zik, xki, yki, zki,
xjk, yjk, zjk, xkj, ykj, zkj;
- point_real xus=NULL;
+ real *xus=NULL;
/* calculate tesselation level */
a = sqrt((((real) densit)-2.)/30.);
tess = max((int) ceil(a), 1);
int make_unsp(int densit, int mode, int * num_dot, int cubus) {
int ndot, ico_cube_cb, i, j, k, l, ijk, tn, tl, tl2;
- point_real xus;
- point_int work;
+ real *xus;
+ int *work;
real x, y, z;
if (xpunsp) free(xpunsp); if (ico_wk) free(ico_wk);
int distribution;
int l;
int maxnei, nnei, last, maxdots=0;
- point_int wkdot=NULL, wkbox=NULL, wkat1=NULL, wkatm=NULL;
+ int *wkdot=NULL, *wkbox=NULL, *wkat1=NULL, *wkatm=NULL;
Neighb *wknb, *ctnb;
int iii1, iii2, iiat, lfnr=0, i_at, j_at;
real dx, dy, dz, dd, ai, aisq, ajsq, aj, as, a;
real xi, yi, zi, xs=0., ys=0., zs=0.;
real dotarea, area, vol=0.;
- point_real xus, dots=NULL, atom_area=NULL;
+ real *xus, *dots=NULL, *atom_area=NULL;
int nxbox, nybox, nzbox, nxy, nxyz;
real xmin, ymin, zmin, xmax, ymax, zmax, ra2max, d, *pco;
/* Added DvdS 2006-07-19 */
distribution = unsp_type(densit);
if (distribution != -last_unsp || last_cubus != 4 ||
(densit != last_densit && densit != last_n_dot)) {
- if (make_unsp(densit, (-distribution), &n_dot, 4)) return 1;
+ if (make_unsp(densit, (-distribution), &n_dot, 4))
+ return 1;
}
xus = xpunsp;
if (mode & FLAG_VOLUME)
vol=0.;
if (mode & FLAG_DOTS) {
- maxdots = 3*n_dot*nat/10;
+ maxdots = (3*n_dot*nat)/10;
snew(dots,maxdots);
lfnr=0;
}
nxyz = nxy*nzbox;
/* box number of atoms */
- snew(wkatm,3*nat);
- wkat1 = wkatm+nat;
- snew(wkdot,n_dot+nxyz+1);
- wkbox = wkdot+n_dot;
+ snew(wkatm,nat);
+ snew(wkat1,nat);
+ snew(wkdot,n_dot);
+ snew(wkbox,nxyz+1);
/* Put the atoms in their boxes */
for (iat_xx=0; (iat_xx<nat); iat_xx++) {
if (debug)
fprintf(debug,"atom %5d on place %5d\n", iat, wkbox[wkat1[iat_xx]]);
}
+
if (debug) {
fprintf(debug,"nsc_dclm: n_dot=%5d ra2max=%9.3f %9.3f\n",
n_dot, ra2max, dotarea);
/* calculate surface for all atoms, step cube-wise */
for (iz=0; iz<nzbox; iz++) {
iii = iz*nxy;
- izs = max(iz-1,0);
- ize = min(iz+2, nzbox);
+ if (box) {
+ izs = iz-1;
+ ize = min(iz+2,izs+nzbox);
+ }
+ else {
+ izs = max(iz-1,0);
+ ize = min(iz+2, nzbox);
+ }
for (iy=0; iy<nybox; iy++) {
ii = iy*nxbox+iii;
- iys = max(iy-1,0);
- iye = min(iy+2, nybox);
+ if (box) {
+ iys = iy-1;
+ iye = min(iy+2,iys+nybox);
+ }
+ else {
+ iys = max(iy-1,0);
+ iye = min(iy+2, nybox);
+ }
for (ix=0; ix<nxbox; ix++) {
i = ii+ix;
iii1=wkbox[i];
iii2=wkbox[i+1];
if (iii1 >= iii2)
continue;
- ixs = max(ix-1,0);
- ixe = min(ix+2, nxbox);
-
+ if (box) {
+ ixs = ix-1;
+ ixe = min(ix+2,ixs+nxbox);
+ }
+ else {
+ ixs = max(ix-1,0);
+ ixe = min(ix+2, nxbox);
+ }
iiat = 0;
/* make intermediate atom list */
for (jz=izs; jz<ize; jz++) {
- jjj = jz*nxy;
+ jjj = ((jz+nzbox) % nzbox)*nxy;
for (jy=iys; jy<iye; jy++) {
- jj = jy*nxbox+jjj;
+ jj = ((jy+nybox) % nybox)*nxbox+jjj;
for (jx=ixs; jx<ixe; jx++) {
- j = jj+jx;
+ j = jj+((jx+nxbox) % nxbox);
for (jat=wkbox[j]; jat<wkbox[j+1]; jat++) {
+ range_check(wkatm[jat],0,nat);
+ range_check(iiat,0,nat);
wkat1[iiat] = wkatm[jat];
iiat++;
} /* end of cycle "jat" */
a = aisq*dotarea* (real) i_ac;
area = area + a;
if (mode & FLAG_ATOM_AREA) {
+ range_check(wkatm[iat],0,nat);
atom_area[wkatm[iat]] = a;
}
if (mode & FLAG_DOTS) {
lfnr++;
if (maxdots <= 3*lfnr+1) {
maxdots = maxdots+n_dot*3;
- dots = (real *) REALLOC(dots, maxdots*sizeof(real));
+ srenew(dots,maxdots);
}
dots[3*lfnr-3] = ai*xus[3*l]+xi;
dots[3*lfnr-2] = ai*xus[1+3*l]+yi;
} /* end of cycle "iy" */
} /* end of cycle "iz" */
- sfree(wkatm); sfree(wkdot); sfree(wknb);
+ sfree(wkatm);
+ sfree(wkat1);
+ sfree(wkdot);
+ sfree(wkbox);
+ sfree(wknb);
if (mode & FLAG_VOLUME) {
vol = vol*FOURPI/(3.* (real) n_dot);
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff