Fixed several minor compiler warnings, and made a new GMXRC script.
AUTOMAKE_OPTIONS = foreign
-SUBDIRS = include src share admin scripts man
+SUBDIRS = src admin scripts share include man
#
# Most files in the config subdir is included automatically when
# problems with it, so just include them all...
EXTRA_DIST = config/depcomp config/ltconfig config/ltcf-c.sh \
- config/ltcf-f77.sh config/config.guess config/config.sub \
+ config/ltcf-f77.sh config/config.guess config/config.sub \
config/install-sh config/missing config/ltmain.sh \
- config/mkinstalldirs
+ config/mkinstalldirs
install-hook:
@echo ""
@echo "Make sure to update your PATH and MANPATH to find the"
@echo "programs and unix manual pages, and possibly LD_LIBRARY_PATH"
@echo "or /etc/ld.so.conf if you are using dynamic libraries."
+ @echo ""
+ @echo "If you want links to the executables in /usr/local/bin,"
+ @echo "you can issue \"make links\" now."
# Shortcuts to construct and install the mdrun executable
mdrun:
- (cd $(top_builddir)/src/gmxlib && $(MAKE))
- (cd $(top_builddir)/src/mdlib && $(MAKE))
- (cd $(top_builddir)/src/kernel && $(MAKE) mdrun)
+ (cd $(top_builddir)/src/gmxlib && $(MAKE) ; exit 0)
+ (cd $(top_builddir)/src/mdlib && $(MAKE) ; exit 0)
+ (cd $(top_builddir)/src/kernel && $(MAKE) mdrun ; exit 0)
install-mdrun:
- (cd $(top_builddir)/src/kernel && $(MAKE) install-mdrun)
+ (cd $(top_builddir)/src/kernel && $(MAKE) install-mdrun ; exit 0)
links:
programs=$(bindir)/*
(cd /usr/local/bin && for i in $(programs); do \
- (test ! -e $$i && $(LN_S) $$i .); \
+ (test ! -e $$i && $(LN_S) $$i . ; exit 0); \
done)
rpm:
- mkdir -p rpm_buildroot/BUILD \
- rpm_buildroot/SPECS \
- rpm_buildroot/SOURCES \
- rpm_buildroot/SRPMS \
- rpm_buildroot/RPMS/i386
- cp -f $(PACKAGE)-$(VERSION).tar.gz rpm_buildroot/SOURCES
- cp -f admin/$(PACKAGE).spec rpm_buildroot/SPECS
- rpm --rcfile /usr/lib/rpm/rpmrc:/etc/rpmrc:admin/rpmrc --clean --ba $(PACKAGE).spec
- cp -f rpm_buildroot/RPMS/i386/*rpm $(top_builddir)
- rm -rf rpm_buildroot
-
+ mkdir -p rpmdir/BUILD \
+ rpmdir/SPECS \
+ rpmdir/SOURCES \
+ rpmdir/SRPMS \
+ rpmdir/RPMS/i386
+ cp -f $(PACKAGE)-$(VERSION).tar.gz rpmdir/SOURCES
+ rpm --buildroot $$PWD/rpmdir/buildroot --clean -bb $(top_srcdir)/admin/$(PACKAGE).spec --define "_topdir $$PWD/rpmdir"
+ @echo "========================================================"
+ @echo "Finished - packages are located under rpmdir/RPMS/i386 !"
+
+
+# Dont try to make rpm and mpi-rpm in parallel.
mpi-rpm:
- mkdir -p rpm_buildroot/BUILD \
- rpm_buildroot/SPECS \
- rpm_buildroot/SOURCES \
- rpm_buildroot/SRPMS \
- rpm_buildroot/RPMS/i386
- cp -f $(PACKAGE)-$(VERSION).tar.gz rpm_buildroot/SOURCES/$(PACKAGE)-mpi-$(VERSION).tar.gz
- cp -f admin/$(PACKAGE)-mpi.spec rpm_buildroot/SPECS
- rpm --rcfile /usr/lib/rpm/rpmrc:/etc/rpmrc:admin/rpmrc --clean --ba $(PACKAGE)-mpi.spec
- cp -f rpm_buildroot/RPMS/i386/*rpm $(top_builddir)
- rm -rf rpm_buildroot
+ mkdir -p rpmdir/BUILD \
+ rpmdir/SPECS \
+ rpmdir/SOURCES \
+ rpmdir/SRPMS \
+ rpmdir/RPMS/i386
+ cp -f $(PACKAGE)-$(VERSION).tar.gz rpmdir/SOURCES/$(PACKAGE)-mpi-$(VERSION).tar.gz
+ rpm --buildroot $$PWD/rpmdir/buildroot-mpi --clean -bb rpm_build/SPECS/$(PACKAGE)-mpi.spec --define "_topdir $$PWD/rpmdir"
+ @echo "========================================================"
+ @echo "Finished - packages are located under rpmdir/RPMS/i386 !"
CLEANFILES = *~ \\\#*
-# aclocal.m4 generated automatically by aclocal 1.4f
+# aclocal.m4 generated automatically by aclocal 1.4h
# Copyright 1994, 1995, 1996, 1997, 1998, 1999, 2000
# Free Software Foundation, Inc.
# Autoconf 2.50 wants to disallow AM_ names. We explicitly allow
# the ones we care about.
ifdef([m4_pattern_allow],
- [m4_pattern_allow([^AM_(C|CPP|CXX|OBJC|F|R|GCJ)FLAGS])])dnl
+ [m4_pattern_allow([^AM_[A-Z]+FLAGS])])dnl
# Some tools Automake needs.
AC_REQUIRE([AM_SANITY_CHECK])dnl
#!/bin/csh -f
+# NB: Put the finished completions in the gromacs-3.0/scripts directory.
+
if ( $#argv < 1 ) then
echo "Error: provide the binary directory as first argument."
+ echo "Completions will be written in the current directory."
exit
endif
set GMXBINDIR = $1
-set out = complete
+set out = completion
set dir = $cwd
-echo Generating tcsh completions
+echo Generating completions for csh, bash and zsh
-if ( -f $out) then
- mv complete \#complete\#
+if ( -f $out.csh) then
+ rm $out.csh
+endif
+if ( -f $out.bash) then
+ rm $out.bash
+endif
+if ( -f $out.zsh) then
+ rm $out.zsh
endif
-touch $out
+touch $out.csh $out.bash $out.zsh
cd $GMXBINDIR
set PROGRAMS = [a-z]*
cd $dir
-echo "if ( "'$shell'" == /bin/tcsh ) then" >> $out
-
foreach program ( $PROGRAMS )
- if ( ( $program != "average" ) && ( $program != "luck" ) && ( $program != mdrun ) && ( $program != nmrun ) && ( $program != xmdrun )) then
+ if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "average" ) && ( $program != "GMXRC" ) && ( $program != "completion.zsh" ) && ( $program != "completion.csh" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) ) then
$GMXBINDIR/$program -man completion >& /dev/null
- cat $program.completion >> $out
- \rm $program.completion
+ cat $program.completion-csh >> $out.csh
+ cat $program.completion-bash >> $out.bash
+ cat $program.completion-zsh >> $out.zsh
+ \rm $program.completion-csh $program.completion-bash $program.completion-zsh
endif
end
-echo "endif" >> $out
-
#last line
+
if ( $#argv < 2 ) then
echo "Error: provide the binary directory as first argument,"
echo "and the location of programs.txt as the second."
+ echo "A html subdirectory will be created in the current dir."
exit
endif
cd $dir
foreach program ( $PROGRAMS )
- if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "luck" ) ) then
+ if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) ) then
echo -n "$program "
cd $HTMLOL
$GMXBINDIR/$program -quiet -man html >& /dev/null
if ( $#argv < 1 ) then
echo "Error: provide the binary directory as first argument."
+ echo "Man pages will be written in the current dir."
exit
endif
cd $dir
foreach program ( $PROGRAMS )
-if ( -x $GMXBINDIR/$program ) then
+if ( ( -x $GMXBINDIR/$program ) && ( $program != "my_dssp" ) && ( $program != "GMXRC" ) && ( $program != "completion.csh" ) && ( $program != "completion.zsh" ) && ( $program != "average" ) && ( $program != "completion.bash" ) && ( $program != "luck" ) ) then
echo -n " $program"
$GMXBINDIR/$program -man nroff >& /dev/null
if ( -f $program.nroff ) mv $program.nroff $program.1
if ( $#argv < 2 ) then
echo "Error: provide the binary directory as first argument,"
echo "and the location of programs.txt as the second."
+ echo "Proglist.tex will be written in the current directory."
exit
endif
set dir = $cwd
set VER = 3.0
-set TEXDIR = $cwd/doc
-set TEXIDX = $TEXDIR/proglist.tex
+set TEXIDX = proglist.tex
set GENERAL = "getting_started:Getting_Started flow:Flow_Chart files:File_Formats mdp_opt:mdp_options"
echo "generating latex page $TEXIDX"
echo "--------------------------------"
-if ( ! -d $TEXDIR ) mkdir $TEXDIR
-
if ( -f $TEXIDX ) \rm $TEXIDX
touch $TEXIDX
ac_help="$ac_help
--with-mpi-environment=VAR only start parallel runs when VAR is set"
ac_help="$ac_help
- --disable-nice disable the nice priority on programs"
-ac_help="$ac_help
- --disable-x86-asm don't build assembly loops for x86"
+ --disable-x86-asm don't build assembly loops on x86"
ac_help="$ac_help
--disable-cpu-optimization no detection or tuning flags for cpu version"
ac_help="$ac_help
--enable-vector create inner loops for a vector machine"
ac_help="$ac_help
- --disable-waterloop-unrolling expand water loops (hack for sgi)"
+ --disable-waterloop-unrolling expand the loops instead (hack for sgi)"
ac_help="$ac_help
--disable-waterwater-loops turn off double unrolled loops (hack for sgi)"
ac_help="$ac_help
fi
echo $ac_n "checking for Cygwin environment""... $ac_c" 1>&6
-echo "configure:582: checking for Cygwin environment" >&5
+echo "configure:580: checking for Cygwin environment" >&5
if eval "test \"`echo '$''{'ac_cv_cygwin'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 587 "configure"
+#line 585 "configure"
#include "confdefs.h"
int main() {
return __CYGWIN__;
; return 0; }
EOF
-if { (eval echo configure:598: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:596: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_cygwin=yes
else
CYGWIN=
test "$ac_cv_cygwin" = yes && CYGWIN=yes
echo $ac_n "checking for mingw32 environment""... $ac_c" 1>&6
-echo "configure:615: checking for mingw32 environment" >&5
+echo "configure:613: checking for mingw32 environment" >&5
if eval "test \"`echo '$''{'ac_cv_mingw32'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 620 "configure"
+#line 618 "configure"
#include "confdefs.h"
int main() {
return __MINGW32__;
; return 0; }
EOF
-if { (eval echo configure:627: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:625: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_mingw32=yes
else
ac_config_sub=$ac_aux_dir/config.sub
ac_configure=$ac_aux_dir/configure # This should be Cygnus configure.
+
+# Make sure we can run config.sub.
+if ${CONFIG_SHELL-/bin/sh} $ac_config_sub sun4 >/dev/null 2>&1; then :
+else { echo "configure: error: can not run $ac_config_sub" 1>&2; exit 1; }
+fi
+
+echo $ac_n "checking host system type""... $ac_c" 1>&6
+echo "configure:669: checking host system type" >&5
+
+host_alias=$host
+case "$host_alias" in
+NONE)
+ case $nonopt in
+ NONE)
+ if host_alias=`${CONFIG_SHELL-/bin/sh} $ac_config_guess`; then :
+ else { echo "configure: error: can not guess host type; you must specify one" 1>&2; exit 1; }
+ fi ;;
+ *) host_alias=$nonopt ;;
+ esac ;;
+esac
+
+host=`${CONFIG_SHELL-/bin/sh} $ac_config_sub $host_alias`
+host_cpu=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
+host_vendor=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
+host_os=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
+echo "$ac_t""$host" 1>&6
+
+
# Find a good install program. We prefer a C program (faster),
# so one script is as good as another. But avoid the broken or
# incompatible versions:
# SVR4 /usr/ucb/install, which tries to use the nonexistent group "staff"
# ./install, which can be erroneously created by make from ./install.sh.
echo $ac_n "checking for a BSD compatible install""... $ac_c" 1>&6
-echo "configure:676: checking for a BSD compatible install" >&5
+echo "configure:702: checking for a BSD compatible install" >&5
if test -z "$INSTALL"; then
if eval "test \"`echo '$''{'ac_cv_path_install'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
test -z "$INSTALL_DATA" && INSTALL_DATA='${INSTALL} -m 644'
echo $ac_n "checking whether build environment is sane""... $ac_c" 1>&6
-echo "configure:729: checking whether build environment is sane" >&5
+echo "configure:755: checking whether build environment is sane" >&5
# Just in case
sleep 1
echo timestamp > conftest.file
echo "configure: warning: ${am_backtick}missing' script is too old or missing" 1>&2
fi
-for ac_prog in mawk gawk nawk awk
+for ac_prog in gawk mawk nawk awk
do
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:801: checking for $ac_word" >&5
+echo "configure:827: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_AWK'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
done
echo $ac_n "checking whether ${MAKE-make} sets \${MAKE}""... $ac_c" 1>&6
-echo "configure:831: checking whether ${MAKE-make} sets \${MAKE}" >&5
+echo "configure:857: checking whether ${MAKE-make} sets \${MAKE}" >&5
set dummy ${MAKE-make}; ac_make=`echo "$2" | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_prog_make_${ac_make}_set'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
-# Make sure we can run config.sub.
-if ${CONFIG_SHELL-/bin/sh} $ac_config_sub sun4 >/dev/null 2>&1; then :
-else { echo "configure: error: can not run $ac_config_sub" 1>&2; exit 1; }
-fi
-
-echo $ac_n "checking host system type""... $ac_c" 1>&6
-echo "configure:963: checking host system type" >&5
-
-host_alias=$host
-case "$host_alias" in
-NONE)
- case $nonopt in
- NONE)
- if host_alias=`${CONFIG_SHELL-/bin/sh} $ac_config_guess`; then :
- else { echo "configure: error: can not guess host type; you must specify one" 1>&2; exit 1; }
- fi ;;
- *) host_alias=$nonopt ;;
- esac ;;
-esac
-
-host=`${CONFIG_SHELL-/bin/sh} $ac_config_sub $host_alias`
-host_cpu=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\1/'`
-host_vendor=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\2/'`
-host_os=`echo $host | sed 's/^\([^-]*\)-\([^-]*\)-\(.*\)$/\3/'`
-echo "$ac_t""$host" 1>&6
-
-
fi
-### Automatic nicing of programs
-# Check whether --enable-nice or --disable-nice was given.
-if test "${enable_nice+set}" = set; then
- enableval="$enable_nice"
- :
-else
- enable_nice=yes
-fi
-
-if test "$enable_nice" = "no"; then
- cat >> confdefs.h <<\EOF
-#define NO_NICE
-EOF
-
-fi
-
-
### X86 assembly code
# Check whether --enable-x86_asm or --disable-x86_asm was given.
if test "${enable_x86_asm+set}" = set; then
fi
+
### Vector machine inner loops
# Check whether --enable-vector or --disable-vector was given.
if test "${enable_vector+set}" = set; then
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1349: checking for $ac_word" >&5
+echo "configure:1332: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_F77'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1384: checking for $ac_word" >&5
+echo "configure:1367: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_F77'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
fi
echo $ac_n "checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) works""... $ac_c" 1>&6
-echo "configure:1417: checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) works" >&5
+echo "configure:1400: checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) works" >&5
ac_ext=f
ac_compile='${F77-f77} -c $FFLAGS conftest.$ac_ext 1>&5'
end
EOF
-if { (eval echo configure:1430: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:1413: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
ac_cv_prog_f77_works=yes
# If we can't run a trivial program, we are probably using a cross compiler.
if (./conftest; exit) 2>/dev/null; then
{ echo "configure: error: installation or configuration problem: Fortran 77 compiler cannot create executables." 1>&2; exit 1; }
fi
echo $ac_n "checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) is a cross-compiler""... $ac_c" 1>&6
-echo "configure:1456: checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) is a cross-compiler" >&5
+echo "configure:1439: checking whether the Fortran 77 compiler ($F77 $FFLAGS $LDFLAGS) is a cross-compiler" >&5
echo "$ac_t""$ac_cv_prog_f77_cross" 1>&6
cross_compiling=$ac_cv_prog_f77_cross
echo $ac_n "checking whether we are using GNU Fortran 77""... $ac_c" 1>&6
-echo "configure:1461: checking whether we are using GNU Fortran 77" >&5
+echo "configure:1444: checking whether we are using GNU Fortran 77" >&5
if eval "test \"`echo '$''{'ac_cv_prog_g77'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
yes
#endif
EOF
-if { ac_try='$F77 -E conftest.fpp'; { (eval echo configure:1470: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; } | egrep yes >/dev/null 2>&1; then
+if { ac_try='$F77 -E conftest.fpp'; { (eval echo configure:1453: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; } | egrep yes >/dev/null 2>&1; then
ac_cv_prog_g77=yes
else
ac_cv_prog_g77=no
ac_save_FFLAGS="$FFLAGS"
FFLAGS=
echo $ac_n "checking whether $F77 accepts -g""... $ac_c" 1>&6
-echo "configure:1485: checking whether $F77 accepts -g" >&5
+echo "configure:1468: checking whether $F77 accepts -g" >&5
if eval "test \"`echo '$''{'ac_cv_prog_f77_g'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1526: checking for $ac_word" >&5
+echo "configure:1509: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "gcc", so it can be a program name with args.
set dummy gcc; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1558: checking for $ac_word" >&5
+echo "configure:1541: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "cc", so it can be a program name with args.
set dummy cc; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1588: checking for $ac_word" >&5
+echo "configure:1571: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "cl", so it can be a program name with args.
set dummy cl; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1639: checking for $ac_word" >&5
+echo "configure:1622: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_CC'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
fi
echo $ac_n "checking whether the C compiler ($CC $CFLAGS $LDFLAGS) works""... $ac_c" 1>&6
-echo "configure:1671: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) works" >&5
+echo "configure:1654: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) works" >&5
ac_ext=c
# CFLAGS is not in ac_cpp because -g, -O, etc. are not valid cpp options.
cat > conftest.$ac_ext << EOF
-#line 1682 "configure"
+#line 1665 "configure"
#include "confdefs.h"
main(){return(0);}
EOF
-if { (eval echo configure:1687: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:1670: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
ac_cv_prog_cc_works=yes
# If we can't run a trivial program, we are probably using a cross compiler.
if (./conftest; exit) 2>/dev/null; then
{ echo "configure: error: installation or configuration problem: C compiler cannot create executables." 1>&2; exit 1; }
fi
echo $ac_n "checking whether the C compiler ($CC $CFLAGS $LDFLAGS) is a cross-compiler""... $ac_c" 1>&6
-echo "configure:1713: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) is a cross-compiler" >&5
+echo "configure:1696: checking whether the C compiler ($CC $CFLAGS $LDFLAGS) is a cross-compiler" >&5
echo "$ac_t""$ac_cv_prog_cc_cross" 1>&6
cross_compiling=$ac_cv_prog_cc_cross
echo $ac_n "checking whether we are using GNU C""... $ac_c" 1>&6
-echo "configure:1718: checking whether we are using GNU C" >&5
+echo "configure:1701: checking whether we are using GNU C" >&5
if eval "test \"`echo '$''{'ac_cv_prog_gcc'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
yes;
#endif
EOF
-if { ac_try='${CC-cc} -E conftest.c'; { (eval echo configure:1727: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; } | egrep yes >/dev/null 2>&1; then
+if { ac_try='${CC-cc} -E conftest.c'; { (eval echo configure:1710: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; } | egrep yes >/dev/null 2>&1; then
ac_cv_prog_gcc=yes
else
ac_cv_prog_gcc=no
ac_save_CFLAGS="$CFLAGS"
CFLAGS=
echo $ac_n "checking whether ${CC-cc} accepts -g""... $ac_c" 1>&6
-echo "configure:1746: checking whether ${CC-cc} accepts -g" >&5
+echo "configure:1729: checking whether ${CC-cc} accepts -g" >&5
if eval "test \"`echo '$''{'ac_cv_prog_cc_g'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking how to run the C preprocessor""... $ac_c" 1>&6
-echo "configure:1779: checking how to run the C preprocessor" >&5
+echo "configure:1762: checking how to run the C preprocessor" >&5
# On Suns, sometimes $CPP names a directory.
if test -n "$CPP" && test -d "$CPP"; then
CPP=
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp.
cat > conftest.$ac_ext <<EOF
-#line 1794 "configure"
+#line 1777 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:1800: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:1783: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
rm -rf conftest*
CPP="${CC-cc} -E -traditional-cpp"
cat > conftest.$ac_ext <<EOF
-#line 1811 "configure"
+#line 1794 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:1817: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:1800: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
rm -rf conftest*
CPP="${CC-cc} -nologo -E"
cat > conftest.$ac_ext <<EOF
-#line 1828 "configure"
+#line 1811 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:1834: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:1817: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
END
# If we don't find an include directive, just comment out the code.
echo $ac_n "checking for style of include used by $am_make""... $ac_c" 1>&6
-echo "configure:1865: checking for style of include used by $am_make" >&5
+echo "configure:1848: checking for style of include used by $am_make" >&5
_am_include='#'
_am_quote=
_am_result=none
echo $ac_n "checking dependency style of $depcc""... $ac_c" 1>&6
-echo "configure:1904: checking dependency style of $depcc" >&5
+echo "configure:1887: checking dependency style of $depcc" >&5
if eval "test \"`echo '$''{'am_cv_CC_dependencies_compiler_type'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "$ac_prog", so it can be a program name with args.
set dummy $ac_prog; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:1984: checking for $ac_word" >&5
+echo "configure:1967: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_MPICC'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# now change the normal cc to the MPI one - see the comment above.
CC=$MPICC
echo $ac_n "checking whether the MPI cc command works""... $ac_c" 1>&6
-echo "configure:2017: checking whether the MPI cc command works" >&5 # be paranoid
+echo "configure:2000: checking whether the MPI cc command works" >&5 # be paranoid
cat > conftest.$ac_ext <<EOF
-#line 2019 "configure"
+#line 2002 "configure"
#include "confdefs.h"
#include <mpi.h>
int main() {
int argc; char **argv; MPI_Init(&argc,&argv);
; return 0; }
EOF
-if { (eval echo configure:2026: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2009: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
else
if test "$enable_fortran" = "yes"; then
echo $ac_n "checking for Fortran 77 libraries""... $ac_c" 1>&6
-echo "configure:2047: checking for Fortran 77 libraries" >&5
+echo "configure:2030: checking for Fortran 77 libraries" >&5
if eval "test \"`echo '$''{'ac_cv_flibs'+set}'`\" = set"; then
echo $ac_n "checking fortran name mangling""... $ac_c" 1>&6
-echo "configure:2206: checking fortran name mangling" >&5
+echo "configure:2189: checking fortran name mangling" >&5
cat > mangle-func.f <<EOF
subroutine foobar()
return
end
EOF
ac_try='$F77 -c $FFLAGS mangle-func.f 1>&5'
-if { (eval echo configure:2216: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; then
+if { (eval echo configure:2199: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; then
ac_try=""
else
echo "configure: failed program was:" >&5
ac_save_LIBS="$LIBS"
LIBS="mangle-func.o $FLIBS $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 2237 "configure"
+#line 2220 "configure"
#include "confdefs.h"
int main() {
foobar();
; return 0; }
EOF
-if { (eval echo configure:2244: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2227: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_f77_mangle_type=lowercase
else
cat conftest.$ac_ext >&5
rm -rf conftest*
cat > conftest.$ac_ext <<EOF
-#line 2252 "configure"
+#line 2235 "configure"
#include "confdefs.h"
int main() {
foobar_();
; return 0; }
EOF
-if { (eval echo configure:2259: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2242: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_f77_mangle_type=lowercase-underscore
else
cat conftest.$ac_ext >&5
rm -rf conftest*
cat > conftest.$ac_ext <<EOF
-#line 2267 "configure"
+#line 2250 "configure"
#include "confdefs.h"
int main() {
FOOBAR();
; return 0; }
EOF
-if { (eval echo configure:2274: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2257: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_f77_mangle_type=uppercase
else
cat conftest.$ac_ext >&5
rm -rf conftest*
cat > conftest.$ac_ext <<EOF
-#line 2282 "configure"
+#line 2265 "configure"
#include "confdefs.h"
int main() {
FOOBAR_();
; return 0; }
EOF
-if { (eval echo configure:2289: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2272: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_f77_mangle_type=uppercase-underscore
else
esac
echo $ac_n "checking whether f77 functions with underscore get an extra underscore""... $ac_c" 1>&6
-echo "configure:2346: checking whether f77 functions with underscore get an extra underscore" >&5
+echo "configure:2329: checking whether f77 functions with underscore get an extra underscore" >&5
ac_ext=c
ac_save_LIBS="$LIBS"
LIBS="mangle-func.o $FLIBS $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 2359 "configure"
+#line 2342 "configure"
#include "confdefs.h"
int main() {
$mangle_try();
; return 0; }
EOF
-if { (eval echo configure:2366: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:2349: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_f77_mangle_underscore=yes;
cat >> confdefs.h <<\EOF
fi
echo $ac_n "checking how to run the C preprocessor""... $ac_c" 1>&6
-echo "configure:2394: checking how to run the C preprocessor" >&5
+echo "configure:2377: checking how to run the C preprocessor" >&5
# On Suns, sometimes $CPP names a directory.
if test -n "$CPP" && test -d "$CPP"; then
CPP=
# On the NeXT, cc -E runs the code through the compiler's parser,
# not just through cpp.
cat > conftest.$ac_ext <<EOF
-#line 2409 "configure"
+#line 2392 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:2415: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:2398: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
rm -rf conftest*
CPP="${CC-cc} -E -traditional-cpp"
cat > conftest.$ac_ext <<EOF
-#line 2426 "configure"
+#line 2409 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:2432: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:2415: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
rm -rf conftest*
CPP="${CC-cc} -nologo -E"
cat > conftest.$ac_ext <<EOF
-#line 2443 "configure"
+#line 2426 "configure"
#include "confdefs.h"
#include <assert.h>
Syntax Error
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:2449: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:2432: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
:
echo "$ac_t""$CPP" 1>&6
-if test "$enable_cpu_tuning" = "yes"; then
+if test "$enable_cpu_optimization" = "yes"; then
echo $ac_n "checking whether $CC accepts -malign-double""... $ac_c" 1>&6
-echo "configure:2772: checking whether $CC accepts -malign-double" >&5
+echo "configure:2755: checking whether $CC accepts -malign-double" >&5
if eval "test \"`echo '$''{'ac_align_double'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $CC accepts -mcpu=$cputype""... $ac_c" 1>&6
-echo "configure:2821: checking whether $CC accepts -mcpu=$cputype" >&5
+echo "configure:2804: checking whether $CC accepts -mcpu=$cputype" >&5
if eval "test \"`echo '$''{'ac_m_cpu_60x'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $CC accepts -mcpu=750""... $ac_c" 1>&6
-echo "configure:2848: checking whether $CC accepts -mcpu=750" >&5
+echo "configure:2831: checking whether $CC accepts -mcpu=750" >&5
if eval "test \"`echo '$''{'ac_m_cpu_750'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $CC accepts -mcpu=powerpc""... $ac_c" 1>&6
-echo "configure:2876: checking whether $CC accepts -mcpu=powerpc" >&5
+echo "configure:2859: checking whether $CC accepts -mcpu=powerpc" >&5
if eval "test \"`echo '$''{'ac_m_cpu_powerpc'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $CC accepts -mpowerpc""... $ac_c" 1>&6
-echo "configure:2904: checking whether $CC accepts -mpowerpc" >&5
+echo "configure:2887: checking whether $CC accepts -mpowerpc" >&5
if eval "test \"`echo '$''{'ac_m_powerpc'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $CC accepts ${CFLAGS}""... $ac_c" 1>&6
-echo "configure:2966: checking whether $CC accepts ${CFLAGS}" >&5
+echo "configure:2949: checking whether $CC accepts ${CFLAGS}" >&5
if eval "test \"`echo '$''{'ac_guessed_cflags'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking whether $F77 accepts ${FFLAGS}""... $ac_c" 1>&6
-echo "configure:3015: checking whether $F77 accepts ${FFLAGS}" >&5
+echo "configure:2998: checking whether $F77 accepts ${FFLAGS}" >&5
if eval "test \"`echo '$''{'ac_guessed_fflags'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
-
# Check x86 asm prerequisites and the capabilities of as
if test "$enable_x86_asm" = "yes"; then
if test "$enable_float" = "no"; then
enable_x86_asm=no
else
echo $ac_n "checking whether as fully supports intel syntax""... $ac_c" 1>&6
-echo "configure:3065: checking whether as fully supports intel syntax" >&5
+echo "configure:3047: checking whether as fully supports intel syntax" >&5
cat > conftest.s << EOF
.intel_syntax noprefix
checkasm:
emms
ret
EOF
- if { ac_try='$CC -c conftest.s'; { (eval echo configure:3075: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; }; then
+ if { ac_try='$CC -c conftest.s'; { (eval echo configure:3057: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }; }; then
echo "$ac_t""yes" 1>&6
else
echo "$ac_t""no" 1>&6
# Extract the first word of "ident", so it can be a program name with args.
set dummy ident; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:3089: checking for $ac_word" >&5
+echo "configure:3071: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_path_IDENT'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# seems as if we have the ident program, but does the
# compiler support it?
echo $ac_n "checking whether the compiler supports ident""... $ac_c" 1>&6
-echo "configure:3126: checking whether the compiler supports ident" >&5
+echo "configure:3108: checking whether the compiler supports ident" >&5
cat > conftest.$ac_ext <<EOF
-#line 3128 "configure"
+#line 3110 "configure"
#include "confdefs.h"
#ident "@(#) file.h 1.1 12/16/92"
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:3133: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:3115: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
fi
echo $ac_n "checking build system type""... $ac_c" 1>&6
-echo "configure:3223: checking build system type" >&5
+echo "configure:3205: checking build system type" >&5
build_alias=$build
case "$build_alias" in
if test "$GCC" = yes; then
# Check if gcc -print-prog-name=ld gives a path.
echo $ac_n "checking for ld used by GCC""... $ac_c" 1>&6
-echo "configure:3252: checking for ld used by GCC" >&5
+echo "configure:3234: checking for ld used by GCC" >&5
case $host in
*-*-mingw*)
# gcc leaves a trailing carriage return which upsets mingw
esac
elif test "$with_gnu_ld" = yes; then
echo $ac_n "checking for GNU ld""... $ac_c" 1>&6
-echo "configure:3282: checking for GNU ld" >&5
+echo "configure:3264: checking for GNU ld" >&5
else
echo $ac_n "checking for non-GNU ld""... $ac_c" 1>&6
-echo "configure:3285: checking for non-GNU ld" >&5
+echo "configure:3267: checking for non-GNU ld" >&5
fi
if eval "test \"`echo '$''{'lt_cv_path_LD'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
fi
test -z "$LD" && { echo "configure: error: no acceptable ld found in \$PATH" 1>&2; exit 1; }
echo $ac_n "checking if the linker ($LD) is GNU ld""... $ac_c" 1>&6
-echo "configure:3320: checking if the linker ($LD) is GNU ld" >&5
+echo "configure:3302: checking if the linker ($LD) is GNU ld" >&5
if eval "test \"`echo '$''{'lt_cv_prog_gnu_ld'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo $ac_n "checking for $LD option to reload object files""... $ac_c" 1>&6
-echo "configure:3337: checking for $LD option to reload object files" >&5
+echo "configure:3319: checking for $LD option to reload object files" >&5
if eval "test \"`echo '$''{'lt_cv_ld_reload_flag'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
test -n "$reload_flag" && reload_flag=" $reload_flag"
echo $ac_n "checking for BSD-compatible nm""... $ac_c" 1>&6
-echo "configure:3349: checking for BSD-compatible nm" >&5
+echo "configure:3331: checking for BSD-compatible nm" >&5
if eval "test \"`echo '$''{'lt_cv_path_NM'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
echo "$ac_t""$NM" 1>&6
echo $ac_n "checking whether ln -s works""... $ac_c" 1>&6
-echo "configure:3387: checking whether ln -s works" >&5
+echo "configure:3369: checking whether ln -s works" >&5
if eval "test \"`echo '$''{'ac_cv_prog_LN_S'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
fi
echo $ac_n "checking how to recognise dependant libraries""... $ac_c" 1>&6
-echo "configure:3408: checking how to recognise dependant libraries" >&5
+echo "configure:3390: checking how to recognise dependant libraries" >&5
if eval "test \"`echo '$''{'lt_cv_deplibs_check_method'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
deplibs_check_method=$lt_cv_deplibs_check_method
echo $ac_n "checking for object suffix""... $ac_c" 1>&6
-echo "configure:3572: checking for object suffix" >&5
+echo "configure:3554: checking for object suffix" >&5
if eval "test \"`echo '$''{'ac_cv_objext'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
rm -f conftest*
echo 'int i = 1;' > conftest.$ac_ext
-if { (eval echo configure:3578: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:3560: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
for ac_file in conftest.*; do
case $ac_file in
*.c) ;;
echo $ac_n "checking for executable suffix""... $ac_c" 1>&6
-echo "configure:3598: checking for executable suffix" >&5
+echo "configure:3580: checking for executable suffix" >&5
if eval "test \"`echo '$''{'ac_cv_exeext'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
rm -f conftest*
echo 'int main () { return 0; }' > conftest.$ac_ext
ac_cv_exeext=
- if { (eval echo configure:3608: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; }; then
+ if { (eval echo configure:3590: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; }; then
for file in conftest.*; do
case $file in
*.c | *.o | *.obj) ;;
file_magic*)
if test "$file_magic_cmd" = '$MAGIC_CMD'; then
echo $ac_n "checking for ${ac_tool_prefix}file""... $ac_c" 1>&6
-echo "configure:3641: checking for ${ac_tool_prefix}file" >&5
+echo "configure:3623: checking for ${ac_tool_prefix}file" >&5
if eval "test \"`echo '$''{'lt_cv_path_MAGIC_CMD'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
if test -z "$lt_cv_path_MAGIC_CMD"; then
if test -n "$ac_tool_prefix"; then
echo $ac_n "checking for file""... $ac_c" 1>&6
-echo "configure:3703: checking for file" >&5
+echo "configure:3685: checking for file" >&5
if eval "test \"`echo '$''{'lt_cv_path_MAGIC_CMD'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "${ac_tool_prefix}ranlib", so it can be a program name with args.
set dummy ${ac_tool_prefix}ranlib; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:3774: checking for $ac_word" >&5
+echo "configure:3756: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_RANLIB'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "ranlib", so it can be a program name with args.
set dummy ranlib; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:3806: checking for $ac_word" >&5
+echo "configure:3788: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_RANLIB'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "${ac_tool_prefix}strip", so it can be a program name with args.
set dummy ${ac_tool_prefix}strip; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:3841: checking for $ac_word" >&5
+echo "configure:3823: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_STRIP'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
# Extract the first word of "strip", so it can be a program name with args.
set dummy strip; ac_word=$2
echo $ac_n "checking for $ac_word""... $ac_c" 1>&6
-echo "configure:3873: checking for $ac_word" >&5
+echo "configure:3855: checking for $ac_word" >&5
if eval "test \"`echo '$''{'ac_cv_prog_STRIP'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
case $host in
*-*-irix6*)
# Find out which ABI we are using.
- echo '#line 3940 "configure"' > conftest.$ac_ext
- if { (eval echo configure:3941: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+ echo '#line 3922 "configure"' > conftest.$ac_ext
+ if { (eval echo configure:3923: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
case `/usr/bin/file conftest.$ac_objext` in
*32-bit*)
LD="${LD-ld} -32"
SAVE_CFLAGS="$CFLAGS"
CFLAGS="$CFLAGS -belf"
echo $ac_n "checking whether the C compiler needs -belf""... $ac_c" 1>&6
-echo "configure:3962: checking whether the C compiler needs -belf" >&5
+echo "configure:3944: checking whether the C compiler needs -belf" >&5
if eval "test \"`echo '$''{'lt_cv_cc_needs_belf'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cross_compiling=$ac_cv_prog_cc_cross
cat > conftest.$ac_ext <<EOF
-#line 3975 "configure"
+#line 3957 "configure"
#include "confdefs.h"
int main() {
; return 0; }
EOF
-if { (eval echo configure:3982: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:3964: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
lt_cv_cc_needs_belf=yes
else
echo $ac_n "checking whether ln -s works""... $ac_c" 1>&6
-echo "configure:4067: checking whether ln -s works" >&5
+echo "configure:4049: checking whether ln -s works" >&5
if eval "test \"`echo '$''{'ac_cv_prog_LN_S'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
-
############################################################################
# Checks for libraries.
############################################################################
echo $ac_n "checking for sqrt in -lm""... $ac_c" 1>&6
-echo "configure:4098: checking for sqrt in -lm" >&5
+echo "configure:4079: checking for sqrt in -lm" >&5
ac_lib_var=`echo m'_'sqrt | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lm $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4106 "configure"
+#line 4087 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
sqrt()
; return 0; }
EOF
-if { (eval echo configure:4117: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4098: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# libm in the link list, thus the test goes after that for libm!
if test "${host_vendor}" = "ibm"; then
echo $ac_n "checking for main in -lxlopt""... $ac_c" 1>&6
-echo "configure:4152: checking for main in -lxlopt" >&5
+echo "configure:4133: checking for main in -lxlopt" >&5
ac_lib_var=`echo xlopt'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lxlopt $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4160 "configure"
+#line 4141 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4167: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4148: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fi
echo $ac_n "checking for main in -lmass""... $ac_c" 1>&6
-echo "configure:4195: checking for main in -lmass" >&5
+echo "configure:4176: checking for main in -lmass" >&5
ac_lib_var=`echo mass'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lmass $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4203 "configure"
+#line 4184 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4210: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4191: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
power4*)
# first check for a power4 lib, then power3, power2.
-echo $ac_n "checking for library containing main""... $ac_c" 1>&6
-echo "configure:4243: checking for library containing main" >&5
-if eval "test \"`echo '$''{'ac_cv_search_main'+set}'`\" = set"; then
+echo $ac_n "checking for library containing vsrsqrt""... $ac_c" 1>&6
+echo "configure:4224: checking for library containing vsrsqrt" >&5
+if eval "test \"`echo '$''{'ac_cv_search_vsrsqrt'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_func_search_save_LIBS="$LIBS"
-ac_cv_search_main="no"
+ac_cv_search_vsrsqrt="no"
cat > conftest.$ac_ext <<EOF
-#line 4250 "configure"
+#line 4231 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4261: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4242: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="none required"
+ ac_cv_search_vsrsqrt="none required"
else
echo "configure: failed program was:" >&5
cat conftest.$ac_ext >&5
fi
rm -f conftest*
-test "$ac_cv_search_main" = "no" && for i in massvp4,massvp3,massvp2,massv; do
+test "$ac_cv_search_vsrsqrt" = "no" && for i in massvp4 massvp3 massvp2 massv; do
LIBS="-l$i $ac_func_search_save_LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4272 "configure"
+#line 4253 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4283: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4264: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="-l$i"
+ ac_cv_search_vsrsqrt="-l$i"
break
else
echo "configure: failed program was:" >&5
LIBS="$ac_func_search_save_LIBS"
fi
-echo "$ac_t""$ac_cv_search_main" 1>&6
-if test "$ac_cv_search_main" != "no"; then
- test "$ac_cv_search_main" = "none required" || LIBS="$ac_cv_search_main $LIBS"
+echo "$ac_t""$ac_cv_search_vsrsqrt" 1>&6
+if test "$ac_cv_search_vsrsqrt" != "no"; then
+ test "$ac_cv_search_vsrsqrt" = "none required" || LIBS="$ac_cv_search_vsrsqrt $LIBS"
vectmass=yes
else :
fi ;;
power3*)
-echo $ac_n "checking for library containing main""... $ac_c" 1>&6
-echo "configure:4306: checking for library containing main" >&5
-if eval "test \"`echo '$''{'ac_cv_search_main'+set}'`\" = set"; then
+echo $ac_n "checking for library containing vsrsqrt""... $ac_c" 1>&6
+echo "configure:4287: checking for library containing vsrsqrt" >&5
+if eval "test \"`echo '$''{'ac_cv_search_vsrsqrt'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_func_search_save_LIBS="$LIBS"
-ac_cv_search_main="no"
+ac_cv_search_vsrsqrt="no"
cat > conftest.$ac_ext <<EOF
-#line 4313 "configure"
+#line 4294 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4324: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4305: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="none required"
+ ac_cv_search_vsrsqrt="none required"
else
echo "configure: failed program was:" >&5
cat conftest.$ac_ext >&5
fi
rm -f conftest*
-test "$ac_cv_search_main" = "no" && for i in massvp3,massvp2,massv; do
+test "$ac_cv_search_vsrsqrt" = "no" && for i in massvp3 massvp2 massv; do
LIBS="-l$i $ac_func_search_save_LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4335 "configure"
+#line 4316 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4346: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4327: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="-l$i"
+ ac_cv_search_vsrsqrt="-l$i"
break
else
echo "configure: failed program was:" >&5
LIBS="$ac_func_search_save_LIBS"
fi
-echo "$ac_t""$ac_cv_search_main" 1>&6
-if test "$ac_cv_search_main" != "no"; then
- test "$ac_cv_search_main" = "none required" || LIBS="$ac_cv_search_main $LIBS"
+echo "$ac_t""$ac_cv_search_vsrsqrt" 1>&6
+if test "$ac_cv_search_vsrsqrt" != "no"; then
+ test "$ac_cv_search_vsrsqrt" = "none required" || LIBS="$ac_cv_search_vsrsqrt $LIBS"
vectmass=yes
else :
fi ;;
power2*)
-echo $ac_n "checking for library containing main""... $ac_c" 1>&6
-echo "configure:4369: checking for library containing main" >&5
-if eval "test \"`echo '$''{'ac_cv_search_main'+set}'`\" = set"; then
+echo $ac_n "checking for library containing vsrsqrt""... $ac_c" 1>&6
+echo "configure:4350: checking for library containing vsrsqrt" >&5
+if eval "test \"`echo '$''{'ac_cv_search_vsrsqrt'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_func_search_save_LIBS="$LIBS"
-ac_cv_search_main="no"
+ac_cv_search_vsrsqrt="no"
cat > conftest.$ac_ext <<EOF
-#line 4376 "configure"
+#line 4357 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4387: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4368: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="none required"
+ ac_cv_search_vsrsqrt="none required"
else
echo "configure: failed program was:" >&5
cat conftest.$ac_ext >&5
fi
rm -f conftest*
-test "$ac_cv_search_main" = "no" && for i in massvp2,massv; do
+test "$ac_cv_search_vsrsqrt" = "no" && for i in massvp2 massv; do
LIBS="-l$i $ac_func_search_save_LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4398 "configure"
+#line 4379 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
builtin and then its argument prototype would still apply. */
-char main();
+char vsrsqrt();
int main() {
-main()
+vsrsqrt()
; return 0; }
EOF
-if { (eval echo configure:4409: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4390: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="-l$i"
+ ac_cv_search_vsrsqrt="-l$i"
break
else
echo "configure: failed program was:" >&5
LIBS="$ac_func_search_save_LIBS"
fi
-echo "$ac_t""$ac_cv_search_main" 1>&6
-if test "$ac_cv_search_main" != "no"; then
- test "$ac_cv_search_main" = "none required" || LIBS="$ac_cv_search_main $LIBS"
+echo "$ac_t""$ac_cv_search_vsrsqrt" 1>&6
+if test "$ac_cv_search_vsrsqrt" != "no"; then
+ test "$ac_cv_search_vsrsqrt" = "none required" || LIBS="$ac_cv_search_vsrsqrt $LIBS"
vectmass=yes
else :
fi ;;
*)
-
-echo $ac_n "checking for library containing main""... $ac_c" 1>&6
-echo "configure:4432: checking for library containing main" >&5
-if eval "test \"`echo '$''{'ac_cv_search_main'+set}'`\" = set"; then
+ echo $ac_n "checking for main in -lvsrsqrt""... $ac_c" 1>&6
+echo "configure:4412: checking for main in -lvsrsqrt" >&5
+ac_lib_var=`echo vsrsqrt'_'main | sed 'y%./+-%__p_%'`
+if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
- ac_func_search_save_LIBS="$LIBS"
-ac_cv_search_main="no"
+ ac_save_LIBS="$LIBS"
+LIBS="-lvsrsqrt $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4439 "configure"
+#line 4420 "configure"
#include "confdefs.h"
-/* Override any gcc2 internal prototype to avoid an error. */
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char main();
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4450: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4427: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
- ac_cv_search_main="none required"
+ eval "ac_cv_lib_$ac_lib_var=yes"
else
echo "configure: failed program was:" >&5
cat conftest.$ac_ext >&5
+ rm -rf conftest*
+ eval "ac_cv_lib_$ac_lib_var=no"
fi
rm -f conftest*
-test "$ac_cv_search_main" = "no" && for i in massv; do
-LIBS="-l$i $ac_func_search_save_LIBS"
-cat > conftest.$ac_ext <<EOF
-#line 4461 "configure"
-#include "confdefs.h"
-/* Override any gcc2 internal prototype to avoid an error. */
-/* We use char because int might match the return type of a gcc2
- builtin and then its argument prototype would still apply. */
-char main();
+LIBS="$ac_save_LIBS"
-int main() {
-main()
-; return 0; }
-EOF
-if { (eval echo configure:4472: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
- rm -rf conftest*
- ac_cv_search_main="-l$i"
-break
-else
- echo "configure: failed program was:" >&5
- cat conftest.$ac_ext >&5
fi
-rm -f conftest*
-done
-LIBS="$ac_func_search_save_LIBS"
+if eval "test \"`echo '$ac_cv_lib_'$ac_lib_var`\" = yes"; then
+ echo "$ac_t""yes" 1>&6
+ vectmass=yes LIBS="$LIBS -lmassv"
+else
+ echo "$ac_t""no" 1>&6
fi
-
-echo "$ac_t""$ac_cv_search_main" 1>&6
-if test "$ac_cv_search_main" != "no"; then
- test "$ac_cv_search_main" = "none required" || LIBS="$ac_cv_search_main $LIBS"
- vectmass=yes
-else :
-
-fi ;;
+ ;;
esac
if test "$vectmass" = "yes"; then
cat >> confdefs.h <<\EOF
ok="no"
# check header doesn't work, since we must use mpicc to get includes, not just /lib/cpp
echo $ac_n "checking for fftw.h""... $ac_c" 1>&6
-echo "configure:4534: checking for fftw.h" >&5
+echo "configure:4489: checking for fftw.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4536 "configure"
+#line 4491 "configure"
#include "confdefs.h"
#include <fftw.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4543: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4498: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=fftw
if test -n "$fftwname"; then
# we cannot run the code since an MPI program might not be allowed on a login node of a supercomputer
cat > conftest.$ac_ext <<EOF
-#line 4561 "configure"
+#line 4516 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:4568: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4523: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ok="yes"
else
if test "$ok" != "yes"; then
xfftwname=${fftwcheckprefix}${fftwname}
echo $ac_n "checking for $xfftwname.h""... $ac_c" 1>&6
-echo "configure:4585: checking for $xfftwname.h" >&5
+echo "configure:4540: checking for $xfftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4587 "configure"
+#line 4542 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4594: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4549: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
else
fi
rm -f conftest*
cat > conftest.$ac_ext <<EOF
-#line 4621 "configure"
+#line 4576 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:4628: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4583: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=$xfftwname
fi
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:4658: checking for main in -l$fftwname" >&5
+echo "configure:4613: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4666 "configure"
+#line 4621 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4673: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4628: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fftwname=${ac_fftw_savedprefix}fftw
echo $ac_n "checking for $fftwname.h""... $ac_c" 1>&6
-echo "configure:4708: checking for $fftwname.h" >&5
+echo "configure:4663: checking for $fftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4710 "configure"
+#line 4665 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4717: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4672: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:4721: checking for main in -l$fftwname" >&5
+echo "configure:4676: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4729 "configure"
+#line 4684 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4736: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4691: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
ok="no"
# check header doesn't work, since we must use mpicc to get includes, not just /lib/cpp
echo $ac_n "checking for rfftw.h""... $ac_c" 1>&6
-echo "configure:4795: checking for rfftw.h" >&5
+echo "configure:4750: checking for rfftw.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4797 "configure"
+#line 4752 "configure"
#include "confdefs.h"
#include <rfftw.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4804: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4759: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=rfftw
if test -n "$fftwname"; then
# we cannot run the code since an MPI program might not be allowed on a login node of a supercomputer
cat > conftest.$ac_ext <<EOF
-#line 4822 "configure"
+#line 4777 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:4829: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4784: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ok="yes"
else
if test "$ok" != "yes"; then
xfftwname=${fftwcheckprefix}${fftwname}
echo $ac_n "checking for $xfftwname.h""... $ac_c" 1>&6
-echo "configure:4846: checking for $xfftwname.h" >&5
+echo "configure:4801: checking for $xfftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4848 "configure"
+#line 4803 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4855: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4810: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
else
fi
rm -f conftest*
cat > conftest.$ac_ext <<EOF
-#line 4882 "configure"
+#line 4837 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:4889: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4844: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=$xfftwname
fi
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:4919: checking for main in -l$fftwname" >&5
+echo "configure:4874: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4927 "configure"
+#line 4882 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4934: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4889: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fftwname=${ac_fftw_savedprefix}rfftw
echo $ac_n "checking for $fftwname.h""... $ac_c" 1>&6
-echo "configure:4969: checking for $fftwname.h" >&5
+echo "configure:4924: checking for $fftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 4971 "configure"
+#line 4926 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:4978: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:4933: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:4982: checking for main in -l$fftwname" >&5
+echo "configure:4937: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 4990 "configure"
+#line 4945 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:4997: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:4952: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
ok="no"
# check header doesn't work, since we must use mpicc to get includes, not just /lib/cpp
echo $ac_n "checking for fftw_mpi.h""... $ac_c" 1>&6
-echo "configure:5058: checking for fftw_mpi.h" >&5
+echo "configure:5013: checking for fftw_mpi.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5060 "configure"
+#line 5015 "configure"
#include "confdefs.h"
#include <fftw_mpi.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5067: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5022: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=fftw_mpi
if test -n "$fftwname"; then
# we cannot run the code since an MPI program might not be allowed on a login node of a supercomputer
cat > conftest.$ac_ext <<EOF
-#line 5085 "configure"
+#line 5040 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:5092: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5047: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ok="yes"
else
if test "$ok" != "yes"; then
xfftwname=${fftwcheckprefix}${fftwname}
echo $ac_n "checking for $xfftwname.h""... $ac_c" 1>&6
-echo "configure:5109: checking for $xfftwname.h" >&5
+echo "configure:5064: checking for $xfftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5111 "configure"
+#line 5066 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5118: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5073: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
else
fi
rm -f conftest*
cat > conftest.$ac_ext <<EOF
-#line 5145 "configure"
+#line 5100 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:5152: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5107: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=$xfftwname
fi
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:5182: checking for main in -l$fftwname" >&5
+echo "configure:5137: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 5190 "configure"
+#line 5145 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:5197: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5152: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fftwname=${ac_fftw_savedprefix}fftw_mpi
echo $ac_n "checking for $fftwname.h""... $ac_c" 1>&6
-echo "configure:5232: checking for $fftwname.h" >&5
+echo "configure:5187: checking for $fftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5234 "configure"
+#line 5189 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5241: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5196: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:5245: checking for main in -l$fftwname" >&5
+echo "configure:5200: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 5253 "configure"
+#line 5208 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:5260: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5215: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
ok="no"
# check header doesn't work, since we must use mpicc to get includes, not just /lib/cpp
echo $ac_n "checking for rfftw_mpi.h""... $ac_c" 1>&6
-echo "configure:5319: checking for rfftw_mpi.h" >&5
+echo "configure:5274: checking for rfftw_mpi.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5321 "configure"
+#line 5276 "configure"
#include "confdefs.h"
#include <rfftw_mpi.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5328: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5283: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=rfftw_mpi
if test -n "$fftwname"; then
# we cannot run the code since an MPI program might not be allowed on a login node of a supercomputer
cat > conftest.$ac_ext <<EOF
-#line 5346 "configure"
+#line 5301 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:5353: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5308: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ok="yes"
else
if test "$ok" != "yes"; then
xfftwname=${fftwcheckprefix}${fftwname}
echo $ac_n "checking for $xfftwname.h""... $ac_c" 1>&6
-echo "configure:5370: checking for $xfftwname.h" >&5
+echo "configure:5325: checking for $xfftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5372 "configure"
+#line 5327 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5379: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5334: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
else
fi
rm -f conftest*
cat > conftest.$ac_ext <<EOF
-#line 5406 "configure"
+#line 5361 "configure"
#include "confdefs.h"
#include <$xfftwname.h>
int main() {
int _array_ [1 - 2 * !((sizeof(fftw_real)) == $realsize)];
; return 0; }
EOF
-if { (eval echo configure:5413: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5368: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
fftwname=$xfftwname
fi
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:5443: checking for main in -l$fftwname" >&5
+echo "configure:5398: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 5451 "configure"
+#line 5406 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:5458: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5413: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fftwname=${ac_fftw_savedprefix}rfftw_mpi
echo $ac_n "checking for $fftwname.h""... $ac_c" 1>&6
-echo "configure:5493: checking for $fftwname.h" >&5
+echo "configure:5448: checking for $fftwname.h" >&5
cat > conftest.$ac_ext <<EOF
-#line 5495 "configure"
+#line 5450 "configure"
#include "confdefs.h"
#include <$fftwname.h>
int main() {
; return 0; }
EOF
-if { (eval echo configure:5502: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5457: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
echo "$ac_t""yes" 1>&6
echo $ac_n "checking for main in -l$fftwname""... $ac_c" 1>&6
-echo "configure:5506: checking for main in -l$fftwname" >&5
+echo "configure:5461: checking for main in -l$fftwname" >&5
ac_lib_var=`echo $fftwname'_'main | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-l$fftwname $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 5514 "configure"
+#line 5469 "configure"
#include "confdefs.h"
int main() {
main()
; return 0; }
EOF
-if { (eval echo configure:5521: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5476: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
do
ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'`
echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6
-echo "configure:5595: checking for $ac_hdr" >&5
+echo "configure:5550: checking for $ac_hdr" >&5
if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5600 "configure"
+#line 5555 "configure"
#include "confdefs.h"
#include <$ac_hdr>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:5605: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:5560: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
EOF
# check for xtc libs if we found headers - on solaris the xdr stuff is in libnsl
echo $ac_n "checking for xdr_float in -lnsl""... $ac_c" 1>&6
-echo "configure:5627: checking for xdr_float in -lnsl" >&5
+echo "configure:5582: checking for xdr_float in -lnsl" >&5
ac_lib_var=`echo nsl'_'xdr_float | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lnsl $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 5635 "configure"
+#line 5590 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
xdr_float()
; return 0; }
EOF
-if { (eval echo configure:5646: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5601: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
fi
cat > conftest.$ac_ext <<EOF
-#line 5674 "configure"
+#line 5629 "configure"
#include "confdefs.h"
#include<rpc/rpc.h>
#include<rpc/xdr.h>
XDR *xd; float f; xdr_float(xd,&f);
; return 0; }
EOF
-if { (eval echo configure:5682: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5637: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
have_xdr=yes
else
# Checks for additional and/or optional functions or libraries.
#AC_FUNC_MALLOC
echo $ac_n "checking for 8-bit clean memcmp""... $ac_c" 1>&6
-echo "configure:5717: checking for 8-bit clean memcmp" >&5
+echo "configure:5672: checking for 8-bit clean memcmp" >&5
if eval "test \"`echo '$''{'ac_cv_func_memcmp_clean'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_cv_func_memcmp_clean=no
else
cat > conftest.$ac_ext <<EOF
-#line 5725 "configure"
+#line 5680 "configure"
#include "confdefs.h"
main()
}
EOF
-if { (eval echo configure:5735: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
+if { (eval echo configure:5690: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
then
ac_cv_func_memcmp_clean=yes
else
test $ac_cv_func_memcmp_clean = no && LIBOBJS="$LIBOBJS memcmp.${ac_objext}"
echo $ac_n "checking return type of signal handlers""... $ac_c" 1>&6
-echo "configure:5753: checking return type of signal handlers" >&5
+echo "configure:5708: checking return type of signal handlers" >&5
if eval "test \"`echo '$''{'ac_cv_type_signal'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5758 "configure"
+#line 5713 "configure"
#include "confdefs.h"
#include <sys/types.h>
#include <signal.h>
int i;
; return 0; }
EOF
-if { (eval echo configure:5775: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:5730: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_type_signal=void
else
echo $ac_n "checking for vprintf""... $ac_c" 1>&6
-echo "configure:5794: checking for vprintf" >&5
+echo "configure:5749: checking for vprintf" >&5
if eval "test \"`echo '$''{'ac_cv_func_vprintf'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5799 "configure"
+#line 5754 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char vprintf(); below. */
; return 0; }
EOF
-if { (eval echo configure:5822: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5777: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_vprintf=yes"
else
if test "$ac_cv_func_vprintf" != yes; then
echo $ac_n "checking for _doprnt""... $ac_c" 1>&6
-echo "configure:5846: checking for _doprnt" >&5
+echo "configure:5801: checking for _doprnt" >&5
if eval "test \"`echo '$''{'ac_cv_func__doprnt'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5851 "configure"
+#line 5806 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char _doprnt(); below. */
; return 0; }
EOF
-if { (eval echo configure:5874: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5829: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func__doprnt=yes"
else
fi
echo $ac_n "checking if malloc debugging is wanted""... $ac_c" 1>&6
-echo "configure:5899: checking if malloc debugging is wanted" >&5
+echo "configure:5854: checking if malloc debugging is wanted" >&5
# Check whether --with-dmalloc or --without-dmalloc was given.
if test "${with_dmalloc+set}" = set; then
withval="$with_dmalloc"
for ac_func in strcasecmp
do
echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
-echo "configure:5922: checking for $ac_func" >&5
+echo "configure:5877: checking for $ac_func" >&5
if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5927 "configure"
+#line 5882 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char $ac_func(); below. */
; return 0; }
EOF
-if { (eval echo configure:5950: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5905: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_$ac_func=yes"
else
for ac_func in strdup
do
echo $ac_n "checking for $ac_func""... $ac_c" 1>&6
-echo "configure:5977: checking for $ac_func" >&5
+echo "configure:5932: checking for $ac_func" >&5
if eval "test \"`echo '$''{'ac_cv_func_$ac_func'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 5982 "configure"
+#line 5937 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char $ac_func(); below. */
; return 0; }
EOF
-if { (eval echo configure:6005: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:5960: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_$ac_func=yes"
else
# Uses ac_ vars as temps to allow command line to override cache and checks.
# --without-x overrides everything else, but does not touch the cache.
echo $ac_n "checking for X""... $ac_c" 1>&6
-echo "configure:6037: checking for X" >&5
+echo "configure:5992: checking for X" >&5
# Check whether --with-x or --without-x was given.
if test "${with_x+set}" = set; then
# First, try using that file with no special directory specified.
cat > conftest.$ac_ext <<EOF
-#line 6099 "configure"
+#line 6054 "configure"
#include "confdefs.h"
#include <$x_direct_test_include>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:6104: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:6059: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
ac_save_LIBS="$LIBS"
LIBS="-l$x_direct_test_library $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6173 "configure"
+#line 6128 "configure"
#include "confdefs.h"
int main() {
${x_direct_test_function}()
; return 0; }
EOF
-if { (eval echo configure:6180: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6135: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
LIBS="$ac_save_LIBS"
# We can link X programs with no special library path.
case "`(uname -sr) 2>/dev/null`" in
"SunOS 5"*)
echo $ac_n "checking whether -R must be followed by a space""... $ac_c" 1>&6
-echo "configure:6286: checking whether -R must be followed by a space" >&5
+echo "configure:6241: checking whether -R must be followed by a space" >&5
ac_xsave_LIBS="$LIBS"; LIBS="$LIBS -R$x_libraries"
cat > conftest.$ac_ext <<EOF
-#line 6289 "configure"
+#line 6244 "configure"
#include "confdefs.h"
int main() {
; return 0; }
EOF
-if { (eval echo configure:6296: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6251: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_R_nospace=yes
else
else
LIBS="$ac_xsave_LIBS -R $x_libraries"
cat > conftest.$ac_ext <<EOF
-#line 6312 "configure"
+#line 6267 "configure"
#include "confdefs.h"
int main() {
; return 0; }
EOF
-if { (eval echo configure:6319: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6274: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
ac_R_space=yes
else
# libraries were built with DECnet support. And karl@cs.umb.edu says
# the Alpha needs dnet_stub (dnet does not exist).
echo $ac_n "checking for dnet_ntoa in -ldnet""... $ac_c" 1>&6
-echo "configure:6351: checking for dnet_ntoa in -ldnet" >&5
+echo "configure:6306: checking for dnet_ntoa in -ldnet" >&5
ac_lib_var=`echo dnet'_'dnet_ntoa | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-ldnet $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6359 "configure"
+#line 6314 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
dnet_ntoa()
; return 0; }
EOF
-if { (eval echo configure:6370: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6325: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
if test $ac_cv_lib_dnet_dnet_ntoa = no; then
echo $ac_n "checking for dnet_ntoa in -ldnet_stub""... $ac_c" 1>&6
-echo "configure:6392: checking for dnet_ntoa in -ldnet_stub" >&5
+echo "configure:6347: checking for dnet_ntoa in -ldnet_stub" >&5
ac_lib_var=`echo dnet_stub'_'dnet_ntoa | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-ldnet_stub $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6400 "configure"
+#line 6355 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
dnet_ntoa()
; return 0; }
EOF
-if { (eval echo configure:6411: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6366: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# The nsl library prevents programs from opening the X display
# on Irix 5.2, according to dickey@clark.net.
echo $ac_n "checking for gethostbyname""... $ac_c" 1>&6
-echo "configure:6440: checking for gethostbyname" >&5
+echo "configure:6395: checking for gethostbyname" >&5
if eval "test \"`echo '$''{'ac_cv_func_gethostbyname'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 6445 "configure"
+#line 6400 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char gethostbyname(); below. */
; return 0; }
EOF
-if { (eval echo configure:6468: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6423: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_gethostbyname=yes"
else
if test $ac_cv_func_gethostbyname = no; then
echo $ac_n "checking for gethostbyname in -lnsl""... $ac_c" 1>&6
-echo "configure:6489: checking for gethostbyname in -lnsl" >&5
+echo "configure:6444: checking for gethostbyname in -lnsl" >&5
ac_lib_var=`echo nsl'_'gethostbyname | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lnsl $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6497 "configure"
+#line 6452 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
gethostbyname()
; return 0; }
EOF
-if { (eval echo configure:6508: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6463: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# -lsocket must be given before -lnsl if both are needed.
# We assume that if connect needs -lnsl, so does gethostbyname.
echo $ac_n "checking for connect""... $ac_c" 1>&6
-echo "configure:6538: checking for connect" >&5
+echo "configure:6493: checking for connect" >&5
if eval "test \"`echo '$''{'ac_cv_func_connect'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 6543 "configure"
+#line 6498 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char connect(); below. */
; return 0; }
EOF
-if { (eval echo configure:6566: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6521: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_connect=yes"
else
if test $ac_cv_func_connect = no; then
echo $ac_n "checking for connect in -lsocket""... $ac_c" 1>&6
-echo "configure:6587: checking for connect in -lsocket" >&5
+echo "configure:6542: checking for connect in -lsocket" >&5
ac_lib_var=`echo socket'_'connect | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lsocket $X_EXTRA_LIBS $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6595 "configure"
+#line 6550 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
connect()
; return 0; }
EOF
-if { (eval echo configure:6606: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6561: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# gomez@mi.uni-erlangen.de says -lposix is necessary on A/UX.
echo $ac_n "checking for remove""... $ac_c" 1>&6
-echo "configure:6630: checking for remove" >&5
+echo "configure:6585: checking for remove" >&5
if eval "test \"`echo '$''{'ac_cv_func_remove'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 6635 "configure"
+#line 6590 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char remove(); below. */
; return 0; }
EOF
-if { (eval echo configure:6658: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6613: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_remove=yes"
else
if test $ac_cv_func_remove = no; then
echo $ac_n "checking for remove in -lposix""... $ac_c" 1>&6
-echo "configure:6679: checking for remove in -lposix" >&5
+echo "configure:6634: checking for remove in -lposix" >&5
ac_lib_var=`echo posix'_'remove | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lposix $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6687 "configure"
+#line 6642 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
remove()
; return 0; }
EOF
-if { (eval echo configure:6698: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6653: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# BSDI BSD/OS 2.1 needs -lipc for XOpenDisplay.
echo $ac_n "checking for shmat""... $ac_c" 1>&6
-echo "configure:6722: checking for shmat" >&5
+echo "configure:6677: checking for shmat" >&5
if eval "test \"`echo '$''{'ac_cv_func_shmat'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 6727 "configure"
+#line 6682 "configure"
#include "confdefs.h"
/* System header to define __stub macros and hopefully few prototypes,
which can conflict with char shmat(); below. */
; return 0; }
EOF
-if { (eval echo configure:6750: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6705: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_func_shmat=yes"
else
if test $ac_cv_func_shmat = no; then
echo $ac_n "checking for shmat in -lipc""... $ac_c" 1>&6
-echo "configure:6771: checking for shmat in -lipc" >&5
+echo "configure:6726: checking for shmat in -lipc" >&5
ac_lib_var=`echo ipc'_'shmat | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lipc $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6779 "configure"
+#line 6734 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
shmat()
; return 0; }
EOF
-if { (eval echo configure:6790: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6745: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
# libraries we check for below, so use a different variable.
# --interran@uluru.Stanford.EDU, kb@cs.umb.edu.
echo $ac_n "checking for IceConnectionNumber in -lICE""... $ac_c" 1>&6
-echo "configure:6823: checking for IceConnectionNumber in -lICE" >&5
+echo "configure:6778: checking for IceConnectionNumber in -lICE" >&5
ac_lib_var=`echo ICE'_'IceConnectionNumber | sed 'y%./+-%__p_%'`
if eval "test \"`echo '$''{'ac_cv_lib_$ac_lib_var'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
ac_save_LIBS="$LIBS"
LIBS="-lICE $X_EXTRA_LIBS $LIBS"
cat > conftest.$ac_ext <<EOF
-#line 6831 "configure"
+#line 6786 "configure"
#include "confdefs.h"
/* Override any gcc2 internal prototype to avoid an error. */
/* We use char because int might match the return type of a gcc2
IceConnectionNumber()
; return 0; }
EOF
-if { (eval echo configure:6842: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6797: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
eval "ac_cv_lib_$ac_lib_var=yes"
else
echo $ac_n "checking for Motif""... $ac_c" 1>&6
-echo "configure:6895: checking for Motif" >&5
+echo "configure:6850: checking for Motif" >&5
#
#
ac_cv_motif_includes="none"
cat > conftest.$ac_ext <<EOF
-#line 6919 "configure"
+#line 6874 "configure"
#include "confdefs.h"
#include <Xm/Xm.h>
int main() {
int a;
; return 0; }
EOF
-if { (eval echo configure:6926: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:6881: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
# Xm/Xm.h is in the standard search path.
#
ac_cv_motif_libraries="none"
cat > conftest.$ac_ext <<EOF
-#line 6991 "configure"
+#line 6946 "configure"
#include "confdefs.h"
#include <Xm/Xm.h>
int main() {
XtToolkitInitialize();
; return 0; }
EOF
-if { (eval echo configure:6998: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
+if { (eval echo configure:6953: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext}; then
rm -rf conftest*
# libXm.a is in the standard search path.
do
ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'`
echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6
-echo "configure:7144: checking for $ac_hdr" >&5
+echo "configure:7099: checking for $ac_hdr" >&5
if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7149 "configure"
+#line 7104 "configure"
#include "confdefs.h"
#include <$ac_hdr>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:7154: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:7109: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
do
ac_safe=`echo "$ac_hdr" | sed 'y%./+-%__p_%'`
echo $ac_n "checking for $ac_hdr""... $ac_c" 1>&6
-echo "configure:7185: checking for $ac_hdr" >&5
+echo "configure:7140: checking for $ac_hdr" >&5
if eval "test \"`echo '$''{'ac_cv_header_$ac_safe'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7190 "configure"
+#line 7145 "configure"
#include "confdefs.h"
#include <$ac_hdr>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:7195: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:7150: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
#####
# Checks for typedefs, structures, and compiler characteristics.
echo $ac_n "checking for working const""... $ac_c" 1>&6
-echo "configure:7225: checking for working const" >&5
+echo "configure:7180: checking for working const" >&5
if eval "test \"`echo '$''{'ac_cv_c_const'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7230 "configure"
+#line 7185 "configure"
#include "confdefs.h"
int main() {
; return 0; }
EOF
-if { (eval echo configure:7279: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:7234: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_c_const=yes
else
fi
echo $ac_n "checking for ANSI C header files""... $ac_c" 1>&6
-echo "configure:7300: checking for ANSI C header files" >&5
+echo "configure:7255: checking for ANSI C header files" >&5
if eval "test \"`echo '$''{'ac_cv_header_stdc'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7305 "configure"
+#line 7260 "configure"
#include "confdefs.h"
#include <stdlib.h>
#include <stdarg.h>
#include <float.h>
EOF
ac_try="$ac_cpp conftest.$ac_ext >/dev/null 2>conftest.out"
-{ (eval echo configure:7313: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
+{ (eval echo configure:7268: \"$ac_try\") 1>&5; (eval $ac_try) 2>&5; }
ac_err=`grep -v '^ *+' conftest.out | grep -v "^conftest.${ac_ext}\$"`
if test -z "$ac_err"; then
rm -rf conftest*
if test $ac_cv_header_stdc = yes; then
# SunOS 4.x string.h does not declare mem*, contrary to ANSI.
cat > conftest.$ac_ext <<EOF
-#line 7330 "configure"
+#line 7285 "configure"
#include "confdefs.h"
#include <string.h>
EOF
if test $ac_cv_header_stdc = yes; then
# ISC 2.0.2 stdlib.h does not declare free, contrary to ANSI.
cat > conftest.$ac_ext <<EOF
-#line 7348 "configure"
+#line 7303 "configure"
#include "confdefs.h"
#include <stdlib.h>
EOF
:
else
cat > conftest.$ac_ext <<EOF
-#line 7369 "configure"
+#line 7324 "configure"
#include "confdefs.h"
#include <ctype.h>
#define ISLOWER(c) ('a' <= (c) && (c) <= 'z')
exit (0); }
EOF
-if { (eval echo configure:7380: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
+if { (eval echo configure:7335: \"$ac_link\") 1>&5; (eval $ac_link) 2>&5; } && test -s conftest${ac_exeext} && (./conftest; exit) 2>/dev/null
then
:
else
fi
echo $ac_n "checking for size_t""... $ac_c" 1>&6
-echo "configure:7404: checking for size_t" >&5
+echo "configure:7359: checking for size_t" >&5
if eval "test \"`echo '$''{'ac_cv_type_size_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7409 "configure"
+#line 7364 "configure"
#include "confdefs.h"
#include <sys/types.h>
#if STDC_HEADERS
fi
echo $ac_n "checking whether struct tm is in sys/time.h or time.h""... $ac_c" 1>&6
-echo "configure:7437: checking whether struct tm is in sys/time.h or time.h" >&5
+echo "configure:7392: checking whether struct tm is in sys/time.h or time.h" >&5
if eval "test \"`echo '$''{'ac_cv_struct_tm'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7442 "configure"
+#line 7397 "configure"
#include "confdefs.h"
#include <sys/types.h>
#include <time.h>
struct tm *tp; tp->tm_sec;
; return 0; }
EOF
-if { (eval echo configure:7450: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:7405: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_struct_tm=time.h
else
fi
echo $ac_n "checking for uid_t in sys/types.h""... $ac_c" 1>&6
-echo "configure:7471: checking for uid_t in sys/types.h" >&5
+echo "configure:7426: checking for uid_t in sys/types.h" >&5
if eval "test \"`echo '$''{'ac_cv_type_uid_t'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
cat > conftest.$ac_ext <<EOF
-#line 7476 "configure"
+#line 7431 "configure"
#include "confdefs.h"
#include <sys/types.h>
EOF
fi
echo $ac_n "checking for inline""... $ac_c" 1>&6
-echo "configure:7505: checking for inline" >&5
+echo "configure:7460: checking for inline" >&5
if eval "test \"`echo '$''{'ac_cv_c_inline'+set}'`\" = set"; then
echo $ac_n "(cached) $ac_c" 1>&6
else
ac_cv_c_inline=no
for ac_kw in inline __inline__ __inline; do
cat > conftest.$ac_ext <<EOF
-#line 7512 "configure"
+#line 7467 "configure"
#include "confdefs.h"
int main() {
} $ac_kw foo() {
; return 0; }
EOF
-if { (eval echo configure:7519: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
+if { (eval echo configure:7474: \"$ac_compile\") 1>&5; (eval $ac_compile) 2>&5; }; then
rm -rf conftest*
ac_cv_c_inline=$ac_kw; break
else
fi
-
-
trap '' 1 2 15
trap 'rm -fr conftest* confdefs* core core.* *.core $ac_clean_files; exit 1' 1 2 15
s%@oldincludedir@%$oldincludedir%g
s%@infodir@%$infodir%g
s%@mandir@%$mandir%g
+s%@host@%$host%g
+s%@host_alias@%$host_alias%g
+s%@host_cpu@%$host_cpu%g
+s%@host_vendor@%$host_vendor%g
+s%@host_os@%$host_os%g
s%@INSTALL_PROGRAM@%$INSTALL_PROGRAM%g
s%@INSTALL_SCRIPT@%$INSTALL_SCRIPT%g
s%@INSTALL_DATA@%$INSTALL_DATA%g
s%@AMDEPBACKSLASH@%$AMDEPBACKSLASH%g
s%@DEPDIR@%$DEPDIR%g
s%@SHARED_VERSION_INFO@%$SHARED_VERSION_INFO%g
-s%@host@%$host%g
-s%@host_alias@%$host_alias%g
-s%@host_cpu@%$host_cpu%g
-s%@host_vendor@%$host_vendor%g
-s%@host_os@%$host_os%g
s%@F77@%$F77%g
s%@CC@%$CC%g
s%@CPP@%$CPP%g
echo ""
echo "* Binaries and libraries for this host will be installed under"
echo " ${show_path}"
-echo " (You can change it with the --exec-prefix option)"
+echo " (You can change it with the --exec-prefix option.)"
if test "$enable_float" = "no" -a "$name_transform_provided" = "no"; then
echo ""
AC_INIT(src/gmxlib/3dview.c)
AC_PREREQ(2.13)
AC_CONFIG_AUX_DIR(config)
+AC_CANONICAL_HOST
+
AM_INIT_AUTOMAKE(gromacs, 3.0)
AC_PREFIX_DEFAULT(/usr/local/gromacs)
AM_CONFIG_HEADER(include/config.h)
SHARED_VERSION_INFO="1:0:0"
AC_SUBST(SHARED_VERSION_INFO)
-AC_CANONICAL_HOST
fi
-### Automatic nicing of programs
-AC_ARG_ENABLE(nice,
- [ --disable-nice disable the nice priority on programs],, enable_nice=yes)
-if test "$enable_nice" = "no"; then
- AC_DEFINE(NO_NICE,,[Turn off the automatic nicing of GROMACS])
-fi
-
-
### X86 assembly code
AC_ARG_ENABLE(x86_asm,
- [ --disable-x86-asm don't build assembly loops for x86],,enable_x86_asm=yes)
+ [ --disable-x86-asm don't build assembly loops on x86],,enable_x86_asm=yes)
case "${host_cpu}" in
i?86) ;;
*) enable_x86_asm=no ;;
AC_ARG_ENABLE(cpu-optimization,
[ --disable-cpu-optimization no detection or tuning flags for cpu version],, enable_cpu_optimization=yes)
+
### Vector machine inner loops
AC_ARG_ENABLE(vector,
[ --enable-vector create inner loops for a vector machine],, enable_vector=no)
### Simplewater hack for SGI - disabled unrolling is the same as simplewater=yes
AC_ARG_ENABLE(waterloop-unrolling,
- [ --disable-waterloop-unrolling expand water loops (hack for sgi)],,
+ [ --disable-waterloop-unrolling expand the loops instead (hack for sgi)],,
[case "${host_cpu}-${host_os}" in
mips*-irix*) enable_waterloop_unrolling=yes ;;
*) enable_waterloop_unrolling=no ;;
AC_PROG_CPP
-if test "$enable_cpu_tuning" = "yes"; then
+if test "$enable_cpu_optimization" = "yes"; then
ACX_DETECT_GMXCPU
else
gmxcpu=""
fi
ACX_COMPILER_MAXOPT
-
# Check x86 asm prerequisites and the capabilities of as
if test "$enable_x86_asm" = "yes"; then
if test "$enable_float" = "no"; then
-
############################################################################
# Checks for libraries.
############################################################################
case "$gmxcpu" in
power4*)
# first check for a power4 lib, then power3, power2.
- AC_SEARCH_LIBS(main,[massvp4,massvp3,massvp2,massv],[vectmass=yes]) ;;
+ AC_SEARCH_LIBS(vsrsqrt,massvp4 massvp3 massvp2 massv,[vectmass=yes]) ;;
power3*)
- AC_SEARCH_LIBS(main,[massvp3,massvp2,massv],[vectmass=yes]) ;;
+ AC_SEARCH_LIBS(vsrsqrt,massvp3 massvp2 massv,[vectmass=yes]) ;;
power2*)
- AC_SEARCH_LIBS(main,[massvp2,massv],[vectmass=yes]) ;;
+ AC_SEARCH_LIBS(vsrsqrt,massvp2 massv,[vectmass=yes]) ;;
*)
- AC_SEARCH_LIBS(main,[massv],[vectmass=yes]) ;;
+ AC_CHECK_LIB(vsrsqrt,main,[vectmass=yes LIBS="$LIBS -lmassv"]) ;;
esac
if test "$vectmass" = "yes"; then
AC_DEFINE(HAVE_LIBMASSV_ANY,,[Use vectorized routines in the IBM MASS library])
exec_prefix="\${prefix}/${host}"
fi
fi
-
-
AC_SUBST(exec_prefix)
AC_OUTPUT([Makefile include/Makefile include/types/Makefile src/Makefile
echo ""
echo "* Binaries and libraries for this host will be installed under"
echo " ${show_path}"
-echo " (You can change it with the --exec-prefix option)"
+echo " (You can change it with the --exec-prefix option.)"
if test "$enable_float" = "no" -a "$name_transform_provided" = "no"; then
echo ""
/* If defined, only start MPI runs when this variable is set */
#undef CHECK_MPI_ENV
-/* Turn off the automatic nicing of GROMACS */
-#undef NO_NICE
-
/* Optimize for a vector architecture */
#undef USE_VECTOR
extern void pr_fns(FILE *fp,int nf,t_filenm tfn[]);
/* Print nf file names and types */
-extern void pr_fopts(FILE *fp,int nf,t_filenm tfn[]);
+extern void pr_fopts(FILE *fp,int nf,t_filenm tfn[], int shell);
/* prints file options in tcsh 'complete' format */
extern void parse_file_args(int *argc,char *argv[],int nf,t_filenm fnm[],
#ifdef CPLUSPLUS
extern "C" {
#endif
-
+
extern void no_buffers(void);
/* Turn off buffering of files (which is default) for debugging purposes */
extern char *libfn(char *file);
-extern FILE *libopen(char *file);
+ extern FILE *libopen(char *file);
/* Open a library file for reading. This looks in the current directory
* first, and then in the library directory. If the file is not found,
* it terminates with a fatal_error
*/
+
+extern bool get_libdir(char *libdir);
extern char *low_libfn(char *file,bool bFatal);
extern void print_pargs(FILE *fp, int npargs,t_pargs pa[]);
-extern void pr_enums(FILE *fp, int npargs,t_pargs pa[]);
+extern void pr_enums(FILE *fp, int npargs,t_pargs pa[],int shell);
#endif
/* no fatal_error when invalid options are encountered */
#define PCA_QUIET (1<<12)
/* does something for non-master mdrun nodes */
-#define PCA_SET_NPRI (1<<13)
-/* set weightless prioriy by default */
+#define PCA_BE_NICE (1<<13)
+/* Default to low priority, unless configured with --disable-nice */
extern int iscan(int argc,char *argv[],int *i);
/* Scan an int from the argument at *i. If the argument length
*/
#endif
-extern void parse_common_args(int *argc,char *argv[],unsigned long Flags,bool bNice,
+extern void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,char **desc,int nbugs,char **bugs);
/* Get arguments from the arg-list. The arguments extracted
enum {
edispcNO, edispcEnerPres, edispcEner, edispcNR
};
+
+/* Shell types, for completion stuff */
+enum {
+ eshellCSH, eshellBASH, eshellZSH, eshellNR
+};
+
-.TH do_dssp 1 "Tue 15 May 2001"
+.TH do_dssp 1 "Thu 5 Jul 2001"
.SH NAME
do_dssp
.B VERSION 3.0
.BI "-b" " time "
.BI "-e" " time "
.BI "-dt" " time "
+.BI "-tu" " enum "
.BI "-[no]w" ""
.BI "-sss" " string "
.SH DESCRIPTION
.BI "-dt" " time" " -1"
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
+,
+.B s
+,
+.B m
+or
+.B h
+
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
.BI "-sss" " string" " HEBT"
Secondary structures for structure count
-.SH DIAGNOSTICS
\- The program is very slow
-.TH editconf 1 "Tue 15 May 2001"
+.TH editconf 1 "Thu 5 Jul 2001"
.SH NAME
editconf
.B VERSION 3.0
.B -label
editconf can add a chain identifier
to a pdb file, which can be useful for analysis with e.g. rasmol.
+
+
+To convert a truncated octrahedron file produced by a package which uses
+a cubic box with the corners cut off (such as Gromos) use:
+
+
+.B editconf -f infile -rotate 0 -45 -35.2644 -bt o -box veclen -o outfile
+
+
+where
+.B veclen
+is the size of the cubic box times sqrt(3)/2.
.SH FILES
.BI "-f" " conf.gro"
.B Input
Choose output from default index groups
.BI "-bt" " enum" " tric"
- Box type for -box and -d: tric, cubic, dodecahedron or octahedron
+ Box type for -box and -d:
+.B tric
+,
+.B cubic
+,
+.B dodecahedron
+or
+.B octahedron
+
.BI "-box" " vector" " 0 0 0"
Box vector lengths (a,b,c)
.BI "-label" " string" " A"
Add chain label for all residues
-.SH DIAGNOSTICS
\- For complex molecules, the periodicity removal routine may break down, in that case you can use trjconv
-.TH eneconv 1 "Tue 15 May 2001"
+.TH eneconv 1 "Thu 5 Jul 2001"
.SH NAME
eneconv
.B VERSION 3.0
.BI "-[no]error" " yes"
Stop on errors in the file
-.SH DIAGNOSTICS
\- 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 "Tue 15 May 2001"
+.TH g_anaeig 1 "Thu 5 Jul 2001"
.SH NAME
g_anaeig
.B VERSION 3.0
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
- Time unit: ps, fs, ns, us, ms, s, m or h
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
-.TH g_analyze 1 "Tue 15 May 2001"
+.TH g_analyze 1 "Thu 5 Jul 2001"
.SH NAME
g_analyze
.B VERSION 3.0
Binwidth for the distribution
.BI "-errbar" " enum" " none"
- Error bars for -av: none, stddev, error or 90
+ Error bars for -av:
+.B none
+,
+.B stddev
+,
+.B error
+or
+.B 90
+
.BI "-[no]power" " no"
Fit data to: b ta
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.TH g_angle 1 "Tue 15 May 2001"
+.TH g_angle 1 "Thu 5 Jul 2001"
.SH NAME
g_angle
.B VERSION 3.0
View output xvg, xpm, eps and pdb files
.BI "-type" " enum" " angle"
- Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans
+ Type of angle to analyse:
+.B angle
+,
+.B dihedral
+,
+.B improper
+or
+.B ryckaert-bellemans
+
.BI "-[no]all" " no"
Plot all angles separately in the averages file, in the order of appearance in the index file.
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
.BI "-endfit" " real" " -1"
Time where to end the exponential fit of the correlation function, -1 is till the end
-.SH DIAGNOSTICS
\- Counting transitions only works for dihedrals with multiplicity 3
-.TH g_bond 1 "Tue 15 May 2001"
+.TH g_bond 1 "Thu 5 Jul 2001"
.SH NAME
g_bond
.B VERSION 3.0
.BI "-[no]aver" " yes"
Sum up distributions
-.SH DIAGNOSTICS
\- It should be possible to get bond information from the topology.
-.TH g_bundle 1 "Tue 15 May 2001"
+.TH g_bundle 1 "Thu 5 Jul 2001"
.SH NAME
g_bundle
.B VERSION 3.0
-.TH g_chi 1 "Tue 15 May 2001"
+.TH g_chi 1 "Thu 5 Jul 2001"
.SH NAME
g_chi
.B VERSION 3.0
perform running average over ndeg degrees for histograms
.BI "-maxchi" " enum" " 0"
- calculate first ndih Chi dihedrals: 0, 1, 2, 3, 4, 5 or 6
+ calculate first ndih Chi dihedrals:
+.B 0
+,
+.B 1
+,
+.B 2
+,
+.B 3
+,
+.B 4
+,
+.B 5
+or
+.B 6
+
.BI "-[no]normhisto" " yes"
Normalize histograms
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
.BI "-endfit" " real" " -1"
Time where to end the exponential fit of the correlation function, -1 is till the end
-.SH DIAGNOSTICS
\- 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.
-.TH g_cluster 1 "Tue 15 May 2001"
+.TH g_cluster 1 "Thu 5 Jul 2001"
.SH NAME
g_cluster
.B VERSION 3.0
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
+(depends on
+.B -max
+and
+.B -keepfree
+).
+
+
+.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.
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
- Time unit: ps, fs, ns, us, ms, s, m or h
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
minimum rms difference with rest of cluster for writing structures
.BI "-method" " enum" " linkage"
- Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos
+ Method for cluster determination:
+.B linkage
+,
+.B jarvis-patrick
+,
+.B monte-carlo
+,
+.B diagonalization
+or
+.B gromos
+
.BI "-[no]binary" " no"
Treat the RMSD matrix as consisting of 0 and 1, where the cut-off is given by -cutoff
-.TH g_confrms 1 "Tue 15 May 2001"
+.TH g_confrms 1 "Thu 5 Jul 2001"
.SH NAME
g_confrms
.B VERSION 3.0
-.TH g_covar 1 "Tue 15 May 2001"
+.TH g_covar 1 "Thu 5 Jul 2001"
.SH NAME
g_covar
.B VERSION 3.0
.BI "-v" " eigenvec.trr "
.BI "-av" " average.pdb "
.BI "-l" " covar.log "
+.BI "-xpm" " covar.xpm "
+.BI "-xpma" " covara.xpm "
.BI "-[no]h" ""
.BI "-[no]X" ""
.BI "-nice" " int "
are written as frames with the eigenvector number as timestamp.
+
The eigenvectors can be analyzed with
.B g_anaeig
.
+
+
+
+Option
+.B -xpm
+writes the whole covariance matrix to an xpm file.
+
+
+
+Option
+.B -xpma
+writes the atomic covariance matrix to an xpm file,
+i.e. for each atom pair the sum of the xx, yy and zz covariances is
+written.
.SH FILES
.BI "-f" " traj.xtc"
.B Input
.B Output
Log file
+.BI "-xpm" " covar.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
+.BI "-xpma" " covara.xpm"
+.B Output, Opt.
+ X PixMap compatible matrix file
+
.SH OTHER OPTIONS
.BI "-[no]h" " no"
Print help info and quit
-.TH g_density 1 "Tue 15 May 2001"
+.TH g_density 1 "Thu 5 Jul 2001"
.SH NAME
g_density
.B VERSION 3.0
.BI "-[no]count" " no"
Only count atoms in slices, no densities. Hydrogens are not counted
-.SH DIAGNOSTICS
\- 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_dielectric 1 "Tue 15 May 2001"
+.TH g_dielectric 1 "Thu 5 Jul 2001"
.SH NAME
g_dielectric
.B VERSION 3.0
Fix parameters at their start values, A (2), tau1 (1), or tau2 (4)
.BI "-ffn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-nsmooth" " int" " 3"
Number of points for smoothing
-.TH g_dih 1 "Tue 15 May 2001"
+.TH g_dih 1 "Thu 5 Jul 2001"
.SH NAME
g_dih
.B VERSION 3.0
.BI "-mult" " int" " -1"
mulitiplicity for dihedral angles (by default read from topology)
-.SH DIAGNOSTICS
\- should not ask for number of frames
-.TH g_dipoles 1 "Tue 15 May 2001"
+.TH g_dipoles 1 "Thu 5 Jul 2001"
.SH NAME
g_dipoles
.B VERSION 3.0
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.TH g_disre 1 "Tue 15 May 2001"
+.TH g_disre 1 "Thu 5 Jul 2001"
.SH NAME
g_disre
.B VERSION 3.0
-.TH g_dist 1 "Tue 15 May 2001"
+.TH g_dist 1 "Thu 5 Jul 2001"
.SH NAME
g_dist
.B VERSION 3.0
-.TH g_dyndom 1 "Tue 15 May 2001"
+.TH g_dyndom 1 "Thu 5 Jul 2001"
.SH NAME
g_dyndom
.B VERSION 3.0
-.TH g_enemat 1 "Tue 15 May 2001"
+.TH g_enemat 1 "Thu 5 Jul 2001"
.SH NAME
g_enemat
.B VERSION 3.0
-.TH g_energy 1 "Tue 15 May 2001"
+.TH g_energy 1 "Thu 5 Jul 2001"
.SH NAME
g_energy
.B VERSION 3.0
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.TH g_gyrate 1 "Tue 15 May 2001"
+.TH g_gyrate 1 "Thu 5 Jul 2001"
.SH NAME
g_gyrate
.B VERSION 3.0
-.TH g_h2order 1 "Tue 15 May 2001"
+.TH g_h2order 1 "Thu 5 Jul 2001"
.SH NAME
g_h2order
.B VERSION 3.0
.BI "-sl" " int" " 0"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
-.SH DIAGNOSTICS
\- 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 "Tue 15 May 2001"
+.TH g_hbond 1 "Thu 5 Jul 2001"
.SH NAME
g_hbond
.B VERSION 3.0
-.TH g_helix 1 "Tue 15 May 2001"
+.TH g_helix 1 "Thu 5 Jul 2001"
.SH NAME
g_helix
.B VERSION 3.0
-.TH g_lie 1 "Tue 15 May 2001"
+.TH g_lie 1 "Thu 5 Jul 2001"
.SH NAME
g_lie
.B VERSION 3.0
.BI "-[no]h" ""
.BI "-[no]X" ""
.BI "-nice" " int "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
.BI "-[no]w" ""
.BI "-Elj" " real "
.BI "-Eqq" " real "
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-b" " time" " -1"
+ First frame (ps) to read from trajectory
+
+.BI "-e" " time" " -1"
+ Last frame (ps) to read from trajectory
+
+.BI "-dt" " time" " -1"
+ Only use frame when t MOD dt = first time (ps)
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
.BI "-Cqq" " real" " 0"
Factor in the LIE equation for Coulomb component of energy
-.BI "-ligand" " string" " "
+.BI "-ligand" " string" " none"
Name of the ligand in the energy file
-.TH g_mdmat 1 "Tue 15 May 2001"
+.TH g_mdmat 1 "Thu 5 Jul 2001"
.SH NAME
g_mdmat
.B VERSION 3.0
-.TH g_mindist 1 "Tue 15 May 2001"
+.TH g_mindist 1 "Thu 5 Jul 2001"
.SH NAME
g_mindist
.B VERSION 3.0
-.TH g_morph 1 "Tue 15 May 2001"
+.TH g_morph 1 "Thu 5 Jul 2001"
.SH NAME
g_morph
.B VERSION 3.0
-.TH g_msd 1 "Tue 15 May 2001"
+.TH g_msd 1 "Thu 5 Jul 2001"
.SH NAME
g_msd
.B VERSION 3.0
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
- Time unit: ps, fs, ns, us, ms, s, m or h
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
.BI "-type" " enum" " no"
- Compute diffusion coefficient in one direction: no, x, y or z
+ Compute diffusion coefficient in one direction:
+.B no
+,
+.B x
+,
+.B y
+or
+.B z
+
.BI "-lateral" " enum" " no"
- Calculate the lateral diffusion in a plane perpendicular to: no, x, y or z
+ Calculate the lateral diffusion in a plane perpendicular to:
+.B no
+,
+.B x
+,
+.B y
+or
+.B z
+
.BI "-ngroup" " int" " 1"
Number of groups to calculate MSD for
-.TH g_nmeig 1 "Tue 15 May 2001"
+.TH g_nmeig 1 "Thu 5 Jul 2001"
.SH NAME
g_nmeig
.B VERSION 3.0
-.TH g_nmens 1 "Tue 15 May 2001"
+.TH g_nmens 1 "Thu 5 Jul 2001"
.SH NAME
g_nmens
.B VERSION 3.0
-.TH g_order 1 "Tue 15 May 2001"
+.TH g_order 1 "Thu 5 Jul 2001"
.SH NAME
g_order
.B VERSION 3.0
View output xvg, xpm, eps and pdb files
.BI "-d" " enum" " z"
- Direction of the normal on the membrane: z, x or y
+ Direction of the normal on the membrane:
+.B z
+,
+.B x
+or
+.B y
+
.BI "-sl" " int" " 1"
Calculate order parameter as function of boxlength, dividing the box in nr slices.
-.TH g_potential 1 "Tue 15 May 2001"
+.TH g_potential 1 "Thu 5 Jul 2001"
.SH NAME
g_potential
.B VERSION 3.0
.BI "-[no]spherical" " no"
Calculate spherical thingie
-.SH DIAGNOSTICS
\- Discarding slices for integration should not be necessary.
-.TH g_rama 1 "Tue 15 May 2001"
+.TH g_rama 1 "Thu 5 Jul 2001"
.SH NAME
g_rama
.B VERSION 3.0
-.TH g_rdf 1 "Tue 15 May 2001"
+.TH g_rdf 1 "Thu 5 Jul 2001"
.SH NAME
g_rdf
.B VERSION 3.0
-.TH g_rms 1 "Tue 15 May 2001"
+.TH g_rms 1 "Thu 5 Jul 2001"
.SH NAME
g_rms
.B VERSION 3.0
Only use frame when t MOD dt = first time (ps)
.BI "-tu" " enum" " ps"
- Time unit: ps, fs, ns, us, ms, s, m or h
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
.BI "-what" " enum" " rmsd"
- Structural difference measure: rmsd, rho or rhosc
+ Structural difference measure:
+.B rmsd
+,
+.B rho
+or
+.B rhosc
+
.BI "-[no]pbc" " yes"
PBC check
-.TH g_rmsdist 1 "Tue 15 May 2001"
+.TH g_rmsdist 1 "Thu 5 Jul 2001"
.SH NAME
g_rmsdist
.B VERSION 3.0
-.TH g_rmsf 1 "Tue 15 May 2001"
+.TH g_rmsf 1 "Thu 5 Jul 2001"
.SH NAME
g_rmsf
.B VERSION 3.0
-.TH g_rotacf 1 "Tue 15 May 2001"
+.TH g_rotacf 1 "Thu 5 Jul 2001"
.SH NAME
g_rotacf
.B VERSION 3.0
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.TH g_saltbr 1 "Tue 15 May 2001"
+.TH g_saltbr 1 "Thu 5 Jul 2001"
.SH NAME
g_saltbr
.B VERSION 3.0
-.TH g_sas 1 "Tue 15 May 2001"
+.TH g_sas 1 "Thu 5 Jul 2001"
.SH NAME
g_sas
.B VERSION 3.0
-.TH g_sgangle 1 "Tue 15 May 2001"
+.TH g_sgangle 1 "Thu 5 Jul 2001"
.SH NAME
g_sgangle
.B VERSION 3.0
-.TH g_sorient 1 "Tue 15 May 2001"
+.TH g_sorient 1 "Thu 5 Jul 2001"
.SH NAME
g_sorient
.B VERSION 3.0
-.TH g_tcaf 1 "Tue 15 May 2001"
+.TH g_tcaf 1 "Thu 5 Jul 2001"
.SH NAME
g_tcaf
.B VERSION 3.0
-.TH g_traj 1 "Tue 15 May 2001"
+.TH g_traj 1 "Thu 5 Jul 2001"
.SH NAME
g_traj
.B VERSION 3.0
Option
.B -ot
-plots the temperature of each group.
-This implies
+plots the temperature of each group,
+provided velocities are present in the trajectory file.This implies
.B -com
.
Option
.B -ekr
-plots the rotational kinetic energy of each group.
+plots the rotational kinetic energy of each group,
+provided velocities are present in the trajectory file.
This implies
.B -com
.
-.TH g_velacc 1 "Tue 15 May 2001"
+.TH g_velacc 1 "Thu 5 Jul 2001"
.SH NAME
g_velacc
.B VERSION 3.0
Normalize ACF
.BI "-P" " enum" " 0"
- Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2 or 3
+ Order of Legendre polynomial for ACF (0 indicates none):
+.B 0
+,
+.B 1
+,
+.B 2
+or
+.B 3
+
.BI "-fitfn" " enum" " none"
- Fit function: none, exp, aexp, exp_exp or vac
+ Fit function:
+.B none
+,
+.B exp
+,
+.B aexp
+,
+.B exp_exp
+or
+.B vac
+
.BI "-ncskip" " int" " 0"
Skip N points in the output file of correlation functions
-.TH genbox 1 "Tue 15 May 2001"
+.TH genbox 1 "Thu 5 Jul 2001"
.SH NAME
genbox
.B VERSION 3.0
.BI "-shell" " real" " 0"
thickness of optional water layer around solute
-.SH DIAGNOSTICS
\- Molecules must be whole in the initial configurations.
\- At the moment -ci only works when inserting one molecule.
-.TH genconf 1 "Tue 15 May 2001"
+.TH genconf 1 "Thu 5 Jul 2001"
.SH NAME
genconf
.B VERSION 3.0
.BI "-[no]renumber" " no"
Renumber residues
-.SH DIAGNOSTICS
\- The program should allow for random displacement off lattice points.
-.TH genion 1 "Tue 15 May 2001"
+.TH genion 1 "Thu 5 Jul 2001"
.SH NAME
genion
.B VERSION 3.0
-.TH genpr 1 "Tue 15 May 2001"
+.TH genpr 1 "Thu 5 Jul 2001"
.SH NAME
genpr
.B VERSION 3.0
-.TH gmxcheck 1 "Tue 15 May 2001"
+.TH gmxcheck 1 "Thu 5 Jul 2001"
.SH NAME
gmxcheck
.B VERSION 3.0
.BI "-[no]X" " no"
Use dialog box GUI to edit command line options
-.BI "-nice" " int" " 19"
+.BI "-nice" " int" " 0"
Set the nicelevel
.BI "-vdwfac" " real" " 0.8"
-.TH gmxdump 1 "Tue 15 May 2001"
+.TH gmxdump 1 "Thu 5 Jul 2001"
.SH NAME
gmxdump
.B VERSION 3.0
-.TH grompp 1 "Tue 15 May 2001"
+.TH grompp 1 "Thu 5 Jul 2001"
.SH NAME
grompp
.B VERSION 3.0
-.TH highway 1 "Tue 15 May 2001"
+.TH highway 1 "Thu 5 Jul 2001"
.SH NAME
highway
.B VERSION 3.0
-.TH make_ndx 1 "Tue 15 May 2001"
+.TH make_ndx 1 "Thu 5 Jul 2001"
.SH NAME
make_ndx
.B VERSION 3.0
-.TH mdrun 1 "Tue 15 May 2001"
+.TH mdrun 1 "Thu 5 Jul 2001"
.SH NAME
mdrun
.B VERSION 3.0
.BI "-[no]X" ""
.BI "-nice" " int "
.BI "-deffnm" " string "
+.BI "-np" " int "
.BI "-[no]v" ""
.BI "-[no]compact" ""
.SH DESCRIPTION
.BI "-deffnm" " string" " "
Set the default filename for all file options
+.BI "-np" " int" " 1"
+ Number of nodes, must be the same as used for grompp
+
.BI "-[no]v" " no"
Be loud and noisy
-.TH mk_angndx 1 "Tue 15 May 2001"
+.TH mk_angndx 1 "Thu 5 Jul 2001"
.SH NAME
mk_angndx
.B VERSION 3.0
Set the nicelevel
.BI "-type" " enum" " angle"
- Type of angle: angle, g96-angle, dihedral, improper, ryckaert-bellemans or phi-psi
+ Type of angle:
+.B angle
+,
+.B g96-angle
+,
+.B dihedral
+,
+.B improper
+,
+.B ryckaert-bellemans
+or
+.B phi-psi
+
-.TH ngmx 1 "Tue 15 May 2001"
+.TH ngmx 1 "Thu 5 Jul 2001"
.SH NAME
ngmx
.B VERSION 3.0
.BI "-dt" " time" " -1"
Only use frame when t MOD dt = first time (ps)
-.SH DIAGNOSTICS
\- Balls option does not work
\- Some times dumps core without a good reason
-.TH nmrun 1 "Tue 15 May 2001"
+.TH nmrun 1 "Thu 5 Jul 2001"
.SH NAME
nmrun
.B VERSION 3.0
.BI "-[no]h" ""
.BI "-[no]X" ""
.BI "-nice" " int "
+.BI "-np" " int "
.BI "-[no]v" ""
.BI "-[no]compact" ""
.SH DESCRIPTION
.BI "-nice" " int" " 19"
Set the nicelevel
+.BI "-np" " int" " 1"
+ Number of nodes, must be the same as used for grompp
+
.BI "-[no]v" " no"
Verbose mode
-.TH pdb2gmx 1 "Tue 15 May 2001"
+.TH pdb2gmx 1 "Thu 5 Jul 2001"
.SH NAME
pdb2gmx
.B VERSION 3.0
Generate all proper dihedrals
.BI "-dummy" " enum" " none"
- Convert atoms to dummy atoms: none, hydrogens or aromatics
+ Convert atoms to dummy atoms:
+.B none
+,
+.B hydrogens
+or
+.B aromatics
+
.BI "-[no]heavyh" " no"
Make hydrogen atoms heavy
-.TH protonate 1 "Tue 15 May 2001"
+.TH protonate 1 "Thu 5 Jul 2001"
.SH NAME
protonate
.B VERSION 3.0
-.TH tpbconv 1 "Tue 15 May 2001"
+.TH tpbconv 1 "Thu 5 Jul 2001"
.SH NAME
tpbconv
.B VERSION 3.0
-.TH trjcat 1 "Tue 15 May 2001"
+.TH trjcat 1 "Thu 5 Jul 2001"
.SH NAME
trjcat
.B VERSION 3.0
-.TH trjconv 1 "Tue 15 May 2001"
+.TH trjconv 1 "Thu 5 Jul 2001"
.SH NAME
trjconv
.B VERSION 3.0
.BI "-trunc" " time "
.BI "-exec" " string "
.BI "-[no]app" ""
+.BI "-split" " time "
.BI "-[no]sep" ""
.SH DESCRIPTION
trjconv can convert trajectory files in many ways:
Last frame (ps) to read from trajectory
.BI "-tu" " enum" " ps"
- Time unit: ps, fs, ns, us, ms, s, m or h
+ Time unit:
+.B ps
+,
+.B fs
+,
+.B ns
+,
+.B us
+,
+.B ms
+,
+.B s
+,
+.B m
+or
+.B h
+
.BI "-[no]w" " no"
View output xvg, xpm, eps and pdb files
Change time step between input frames (ps)
.BI "-pbc" " enum" " none"
- PBC treatment: none, whole, inbox or nojump
+ PBC treatment:
+.B none
+,
+.B whole
+,
+.B inbox
+or
+.B nojump
+
.BI "-ur" " enum" " rect"
- Unit-cell representation: rect, tric or compact
+ Unit-cell representation:
+.B rect
+,
+.B tric
+or
+.B compact
+
.BI "-[no]center" " no"
Center atoms in box
.BI "-[no]app" " no"
Append output
+.BI "-split" " time" " 0"
+ Start writing new file when t MOD split = first time (ps)
+
.BI "-[no]sep" " no"
Write each frame to a separate .gro or .pdb file
-.TH trjorder 1 "Tue 15 May 2001"
+.TH trjorder 1 "Thu 5 Jul 2001"
.SH NAME
trjorder
.B VERSION 3.0
-.TH wheel 1 "Tue 15 May 2001"
+.TH wheel 1 "Thu 5 Jul 2001"
.SH NAME
wheel
.B VERSION 3.0
-.TH x2top 1 "Tue 15 May 2001"
+.TH x2top 1 "Thu 5 Jul 2001"
.SH NAME
x2top
.B VERSION 3.0
.BI "-name" " string" " ICE"
Name of your molecule
-.SH DIAGNOSTICS
\- The atom type selection is primitive. Virtually no chemical knowledge is used
\- Periodic boundary conditions screw up the bonding
-.TH xpm2ps 1 "Tue 15 May 2001"
+.TH xpm2ps 1 "Thu 5 Jul 2001"
.SH NAME
xpm2ps
.B VERSION 3.0
.BI "-[no]w" ""
.BI "-[no]frame" ""
.BI "-title" " enum "
+.BI "-[no]yonce" ""
.BI "-legend" " enum "
.BI "-diag" " enum "
+.BI "-combine" " enum "
.BI "-bx" " real "
.BI "-by" " real "
.BI "-rainbow" " enum "
+.BI "-gradient" " vector "
.BI "-skip" " int "
.BI "-[no]zeroline" ""
.SH DESCRIPTION
.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
+a red gradient for negative numbers and a blue for positive.
If the color coding and legend labels of both matrices are identical,
Display frame, ticks, labels, title and legend
.BI "-title" " enum" " top"
- Show title at: top, ylabel or none
+ Show title at:
+.B top
+,
+.B once
+,
+.B ylabel
+or
+.B none
+
+
+.BI "-[no]yonce" " no"
+ Show y-label only once
.BI "-legend" " enum" " both"
- Show legend: both, first, second or none
+ Show legend:
+.B both
+,
+.B first
+,
+.B second
+or
+.B none
+
.BI "-diag" " enum" " first"
- Diagonal: first, second or none
+ Diagonal:
+.B first
+,
+.B second
+or
+.B none
+
+
+.BI "-combine" " enum" " halves"
+ Combine two matrices:
+.B halves
+,
+.B add
+,
+.B sub
+,
+.B mult
+or
+.B div
+
.BI "-bx" " real" " 0"
Box x-size (also y-size when -by is not set)
Box y-size
.BI "-rainbow" " enum" " no"
- Rainbow colors, convert white to: no, blue or red
+ Rainbow colors, convert white to:
+.B no
+,
+.B blue
+or
+.B red
+
+
+.BI "-gradient" " vector" " 0 0 0"
+ Re-scale colormap to a smooth gradient from white {1,1,1} to {r,g,b}
.BI "-skip" " int" " 1"
only write out every nr-th row and column
-.TH xrama 1 "Tue 15 May 2001"
+.TH xrama 1 "Thu 5 Jul 2001"
.SH NAME
xrama
.B VERSION 3.0
EXTRA_SCRIPTS = grompplog2top make_gromos_nb.pl make_gromos_rtp.py \
make_gromos_bon.pl make_gromos_rtp.pl
+
+bin_SCRIPTS = GMXRC completion.csh completion.bash completion.zsh
+
+EXTRA_DIST = GMXRC.in completion.csh completion.bash completion.zsh \
+ grompplog2top make_gromos_nb.pl make_gromos_rtp.py \
+ make_gromos_bon.pl make_gromos_rtp.pl
+
+GMXRC: GMXRC.in
+ cat $(srcdir)/GMXRC.in | sed 's,@libdir\@,$(libdir),' | \
+ sed 's,@bindir\@,$(bindir),' | \
+ sed 's,@mandir\@,$(mandir),' >$@
+
+CLEANFILES = GMXRC \\\#* *~
+
+
+
+
+
+
bench.gif flow_hline.gif \
flow_right.gif manual.gif \
charts_down.gif flow_left.gif \
- flow_rightleftdown.gif rainbow.gif \
+ flow_rightleftdown.gif gmxlogo_small.jpg \
charts_up.gif flow_leftright.gif \
flow_uprightleft.gif software.gif \
faq.gif flow_leftrightdown.gif \
<table WIDTH="800" NOSAVE NOBORDER >
<tr NOSAVE>
<td WIDTH="120" HEIGHT="140" NOSAVE><a href="http://www.gromacs.org/"><img SRC="
-images/gmxlogo_small.jpg" BORDER=0 height=133 width=116></a></td>
+gif/gmxlogo_small.jpg" BORDER=0 height=133 width=116></a></td>
<td ALIGN=LEFT VALIGN=TOP WIDTH=480 NOSAVE>
<br><br>
<br><br>
<A HREF="gmxfaq.html">FAQ</a>
<br>
-<br><A HREF="http://www.gromacs.org">GROMACS homepage</A>
</TD>
<TD VALIGN=top WIDTH=75%>
<h3>Programs</h3>
<A HREF="online/options.html">Options</a>
<br>
<br><a href=online/average.html>average</a>
+<br><a href=online/completion.bash.html>completion.bash</a>
+<br><a href=online/completion.csh.html>completion.csh</a>
+<br><a href=online/completion.zsh.html>completion.zsh</a>
<br><a href=online/do_dssp.html>do_dssp</a>
<br><a href=online/editconf.html>editconf</a>
<br><a href=online/eneconv.html>eneconv</a>
<br><a href=online/g_disre.html>g_disre</a>
<br><a href=online/g_dist.html>g_dist</a>
<br><a href=online/g_dyndom.html>g_dyndom</a>
-<br><a href=online/genbox.html>genbox</a>
-<br><a href=online/genconf.html>genconf</a>
<br><a href=online/g_enemat.html>g_enemat</a>
<br><a href=online/g_energy.html>g_energy</a>
-<br><a href=online/genion.html>genion</a>
-<br><a href=online/genpr.html>genpr</a>
<br><a href=online/g_gyrate.html>g_gyrate</a>
<br><a href=online/g_h2order.html>g_h2order</a>
<br><a href=online/g_hbond.html>g_hbond</a>
<br><a href=online/g_mindist.html>g_mindist</a>
<br><a href=online/g_morph.html>g_morph</a>
<br><a href=online/g_msd.html>g_msd</a>
-<br><a href=online/gmxcheck.html>gmxcheck</a>
-<br><a href=online/gmxdump.html>gmxdump</a>
<br><a href=online/g_nmeig.html>g_nmeig</a>
<br><a href=online/g_nmens.html>g_nmens</a>
<br><a href=online/g_order.html>g_order</a>
<br><a href=online/g_rms.html>g_rms</a>
<br><a href=online/g_rmsdist.html>g_rmsdist</a>
<br><a href=online/g_rmsf.html>g_rmsf</a>
-<br><a href=online/grompp.html>grompp</a>
<br><a href=online/g_rotacf.html>g_rotacf</a>
<br><a href=online/g_saltbr.html>g_saltbr</a>
<br><a href=online/g_sas.html>g_sas</a>
<br><a href=online/g_tcaf.html>g_tcaf</a>
<br><a href=online/g_traj.html>g_traj</a>
<br><a href=online/g_velacc.html>g_velacc</a>
+<br><a href=online/genbox.html>genbox</a>
+<br><a href=online/genconf.html>genconf</a>
+<br><a href=online/genion.html>genion</a>
+<br><a href=online/genpr.html>genpr</a>
+<br><a href=online/gmxcheck.html>gmxcheck</a>
+<br><a href=online/gmxdump.html>gmxdump</a>
+<br><a href=online/grompp.html>grompp</a>
<br><a href=online/highway.html>highway</a>
<br><a href=online/luck.html>luck</a>
<br><a href=online/make_ndx.html>make_ndx</a>
-<HTML>/n<HEAD>/n<TITLE>do_dssp</TITLE>
+<HTML>
+<HEAD>
+<TITLE>do_dssp</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
do_dssp
reads a trajectory file and computes the secondary structure for
each time frame
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>
-<H3>Diagnostics</H3>
<UL>
<LI>The program is very slow
</UL>
-<HTML>/n<HEAD>/n<TITLE>editconf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>editconf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
editconf converts generic structure format to <tt>.<a href="gro.html">gro</a></tt>, <tt>.<a href="g96.html">g96</a></tt>
or <tt>.<a href="pdb.html">pdb</a></tt>.
<p>
<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: tric, cubic, dodecahedron or octahedron </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>-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>-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>Diagnostics</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>
-<HTML>/n<HEAD>/n<TITLE>eneconv</TITLE>
+<HTML>
+<HEAD>
+<TITLE>eneconv</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
When <tt>-f</tt> is <it>not</it> specified:<br>
Concatenates several energy files in sorted order.
In case of double time frames the one
<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>Diagnostics</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>
-<HTML>/n<HEAD>/n<TITLE>g_anaeig</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_anaeig</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
<tt>g_anaeig</tt> analyzes eigenvectors. The eigenvectors can be of a
covariance matrix (<tt><a href="g_covar.html">g_covar</a></tt>) or of a Normal Modes anaysis
(<tt><a href="g_nmeig.html">g_nmeig</a></tt>).<p>
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</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> -1</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> -1</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: ps, fs, ns, us, ms, s, m or h </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>-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>
-<HTML>/n<HEAD>/n<TITLE>g_analyze</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_analyze</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_analyze reads an ascii file and analyzes data sets.
A line in the input file may start with a time
(see option <tt>-time</tt>) and any number of y values may follow.
<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>-errbar</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Error bars for -av: none, stddev, error or 90 </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]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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
-<HTML>/n<HEAD>/n<TITLE>g_angle</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_angle</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_angle computes the angle distribution for a number of angles
or dihedrals. This way you can check whether your simulation
is correct. With option -ov you can plot the average angle of
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>angle</tt> </TD><TD> Type of angle to analyse: angle, dihedral, improper or ryckaert-bellemans </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>-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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>Counting transitions only works for dihedrals with multiplicity 3
</UL>
-<HTML>/n<HEAD>/n<TITLE>g_bond</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_bond</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_bond makes a distribution of bond lengths. If all is well a
gaussian distribution should be made when using a harmonic potential.
bonds are read from a single group in the index file in order i1-j1
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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> Sum up distributions </TD></TD>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>It should be possible to get bond information from the topology.
</UL>
-<HTML>/n<HEAD>/n<TITLE>g_bundle</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_bundle</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_bundle analyzes bundles of axes. The axes can be for instance
helix axes. The program reads two index groups and divides both
of them in <tt>-na</tt> parts. The groups define the tops and
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </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>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>g_chi</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_chi</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_chi computes phi, psi, omega and chi dihedrals for all your
amino acid backbone and sidechains.
It can compute dihedral angle as a function of time, and as
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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> 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]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]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>-run</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> perform running average over ndeg degrees for histograms </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: 0, 1, 2, 3, 4, 5 or 6 </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>-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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
</TABLE>
<P>
-<H3>Diagnostics</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.
</UL>
-<HTML>/n<HEAD>/n<TITLE>g_cluster</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_cluster</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
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 <tt>-dm</tt> option.
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</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> -1</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> -1</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: ps, fs, ns, us, ms, s, m or h </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]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>-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>-method</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>linkage</tt> </TD><TD> Method for cluster determination: linkage, jarvis-patrick, monte-carlo, diagonalization or gromos </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>-[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>
-<HTML>/n<HEAD>/n<TITLE>g_confrms</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_confrms</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_confrms computes the root mean square deviation (RMSD) of two
structures after LSQ fitting the second structure on the first one.
The two structures do NOT need to have the same number of atoms,
-<HTML>/n<HEAD>/n<TITLE>g_covar</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_covar</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
<tt>g_covar</tt> calculates and diagonalizes the (mass-weighted)
covariance matrix.
All structures are fitted to the structure in the structure file.
the reference structure for the fit is written first with t=-1.
The average (or reference when <tt>-ref</tt> is used) structure is
written with t=0, the eigenvectors
-are written as frames with the eigenvector number as timestamp.<p>
+are written as frames with the eigenvector number as timestamp.
+<p>
The eigenvectors can be analyzed with <tt><a href="g_anaeig.html">g_anaeig</a></tt>.
+<p>
+Option <tt>-<a href="xpm.html">xpm</a></tt> writes the whole covariance matrix to an <a href="xpm.html">xpm</a> file.
+<p>
+Option <tt>-xpma</tt> writes the atomic covariance matrix to an <a href="xpm.html">xpm</a> file,
+i.e. for each atom pair the sum of the xx, yy and zz covariances is
+written.
<P>
<H3>Files</H3>
<TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
<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> </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>-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>
+<TR><TD ALIGN=RIGHT> <b><tt>-xpma</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xpm.html"> covara.xpm</a></tt> </TD><TD> Output, Opt. </TD><TD> X PixMap compatible matrix file </TD></TR>
</TABLE>
<P>
<H3>Other options</H3>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </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>
-<HTML>/n<HEAD>/n<TITLE>g_density</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_density</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Compute partial densities across the box, using an index file. Densities
in gram/cubic centimeter, number densities or electron densities can be
calculated. For electron densities, each atom is weighed by its atomic
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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]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>
</TABLE>
<P>
-<H3>Diagnostics</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.
-<HTML>/n<HEAD>/n<TITLE>g_dielectric</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_dielectric</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
dielectric calculates frequency dependent dielectric constants
from the autocorrelation function of the total dipole moment in
your simulation. This ACF can be generated by <a href="g_dipoles.html">g_dipoles</a>.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>-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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
</TABLE>
<P>
-<HTML>/n<HEAD>/n<TITLE>g_dih</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_dih</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_dih can do two things. The default is to analyze dihedral transitions
by merely computing all the dihedral angles defined in your topology
for the whole trajectory. When a dihedral flips over to another minimum
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>
-<H3>Diagnostics</H3>
<UL>
<LI>should not ask for number of frames
</UL>
-<HTML>/n<HEAD>/n<TITLE>g_dipoles</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_dipoles</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>-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>-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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
-<HTML>/n<HEAD>/n<TITLE>g_disre</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_disre</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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. The program allways
computes the instantaneous violations rather than time-averaged,
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-ntop</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>6</tt> </TD><TD> Number of large violations that are stored in the log file every step </TD></TD>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>g_dist</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_dist</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_dist can calculate the distance between the centers of mass of two
groups of atoms as a function of time. The total distance and its
x, y and z components are plotted.<p>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </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>
-<HTML>/n<HEAD>/n<TITLE>g_dyndom</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_dyndom</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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
It reads the coordinates, and the coordinates of the rotation axis
-<HTML>/n<HEAD>/n<TITLE>g_enemat</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_enemat</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_enemat extracts an energy matrix from an energy file.
With <b>-groups</b> a file must be supplied with on each
line a group to be used. For these groups a matrices of
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_energy</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_energy</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_energy extracts energy components or distance restraint
data from an energy file. The user is prompted to interactively
select the energy terms she wants.<p>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) to read from trajectory </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 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> -1</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]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>-[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>-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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
-<HTML>/n<HEAD>/n<TITLE>g_gyrate</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_gyrate</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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.
<P>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_h2order</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_h2order</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Compute the orientation of water molecules with respect to the normal
of the box. The program determines the average cosine of the angle
between de dipole moment of water and an axis of the box. The box is
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>Diagnostics</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>
-<HTML>/n<HEAD>/n<TITLE>g_hbond</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_hbond</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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
(zero is extended) and the distance Hydrogen - Acceptor.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </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> 60</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> 0.25</tt> </TD><TD> Cutoff radius (nm, Hydrogen - Acceptor) </TD></TD>
-<HTML>/n<HEAD>/n<TITLE>g_helix</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_helix</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_helix computes all kind of helix properties. First, the peptide
is checked to find the longest helical part. This is determined by
Hydrogen bonds and Phi/Psi angles.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>
-<HTML>/n<HEAD>/n<TITLE>g_lie</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_lie</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_lie computes a free energy estimate based on an energy analysis
from. One needs an energy file with the following components:
Coul (A-B) LJ-SR (A-B) etc.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</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> -1</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> -1</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>-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</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></tt> </TD><TD> Name of the ligand in the energy file </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>
<hr>
-<HTML>/n<HEAD>/n<TITLE>g_mdmat</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_mdmat</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_mdmat makes distance matrices consisting of the smallest distance
between residue pairs. With -frames these distance matrices can be
stored as a function
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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> 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>
-<HTML>/n<HEAD>/n<TITLE>g_mindist</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_mindist</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_mindist computes the distance between one group and a number of
other groups.
Both the minimum distance and the number of contacts within a given
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>-d</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0.6</tt> </TD><TD> Distance for contacts </TD></TD>
-<HTML>/n<HEAD>/n<TITLE>g_morph</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_morph</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_morph does a linear interpolation of conformations in order to
create intermediates. Of course these are completely unphysical, but
that you may try to justify yourself. Output is in the form of a
-<HTML>/n<HEAD>/n<TITLE>g_msd</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_msd</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_msd computes the mean square displacement (MSD) of atoms from
their initial positions. This provides an easy way to compute
the diffusion constant using the Einstein relation.
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</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> -1</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> -1</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: ps, fs, ns, us, ms, s, m or h </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>-type</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>no</tt> </TD><TD> Compute diffusion coefficient in one direction: no, x, y or z </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: no, x, y or z </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>-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> 0</tt> </TD><TD> Time between restarting points in trajectory (ps) </TD></TD>
-<HTML>/n<HEAD>/n<TITLE>g_nmeig</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_nmeig</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_nmeig calculates the eigenvectors/values of a (Hessian) matrix,
which can be calculated with <tt><a href="nmrun.html">nmrun</a></tt>.
The eigenvectors are written to a trajectory file (<tt>-v</tt>).
-<HTML>/n<HEAD>/n<TITLE>g_nmens</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_nmens</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
<tt>g_nmens</tt> generates an ensemble around an average structure
in a subspace which is defined by a set of normal modes (eigenvectors).
The eigenvectors are assumed to be mass-weighted.
-<HTML>/n<HEAD>/n<TITLE>g_order</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_order</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Compute the order parameter per atom for carbon tails. For atom i the
vector i-1, i+1 is used together with an axis. The index file has to contain
a group with all equivalent atoms in all tails for each atom the
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-d</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>z</tt> </TD><TD> Direction of the normal on the membrane: z, x or y </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>
-<HTML>/n<HEAD>/n<TITLE>g_potential</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_potential</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
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
<P>
<H3>Files</H3>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>-[no]spherical</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Calculate spherical thingie </TD></TD>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>Discarding slices for integration should not be necessary.
</UL>
-<HTML>/n<HEAD>/n<TITLE>g_rama</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rama</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_rama selects the Phi/Psi dihedral combinations from your topology file
and computes these as a function of time.
Using simple Unix tools such as <it>grep</it> you can select out
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>
</TABLE>
<P>
-<HTML>/n<HEAD>/n<TITLE>g_rdf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rdf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
The structure of liquids can be studied by either neutron or X-ray
scattering. The most common way to describe liquid structure is by a
radial distribution function. However, this is not easy to obtain from
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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> 0.001</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>
-<HTML>/n<HEAD>/n<TITLE>g_rms</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rms</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_rms compares two structures by computing the root mean square
deviation (RMSD), the size-independent 'rho' similarity parameter
(rho) or the scaled rho (rhosc),
<TR><TD ALIGN=RIGHT> <b><tt>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt> -1</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> -1</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> -1</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: ps, fs, ns, us, ms, s, m or h </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>-what</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>rmsd</tt> </TD><TD> Structural difference measure: rmsd, rho or rhosc </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]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> yes</tt> </TD><TD> Fit to reference structure </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>
-<HTML>/n<HEAD>/n<TITLE>g_rmsdist</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rmsdist</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_rmsdist computes the root mean square deviation of atom distances,
which has the advantage that no fit is needed like in standard RMS
deviation as computed by <a href="g_rms.html">g_rms</a>.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>
-<HTML>/n<HEAD>/n<TITLE>g_rmsf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rmsf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_rotacf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_rotacf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_rotacf calculates the rotational correlation function
for molecules. Three atoms (i,j,k) must be given in the index
file, defining two vectors ij and jk. The rotational acf
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
-<HTML>/n<HEAD>/n<TITLE>g_saltbr</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_saltbr</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_saltbr plots the difference 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>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>
-<HTML>/n<HEAD>/n<TITLE>g_sas</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_sas</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_sas computes hydrophobic and total solvent accessible surface area.
As a side effect the Connolly surface can be generated as well in
a <a href="pdb.html">pdb</a> file where the nodes are represented as atoms and the vertices
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>-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>-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>
-<HTML>/n<HEAD>/n<TITLE>g_sgangle</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_sgangle</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Compute the angle and distance between two groups.
The groups are defined by a number of atoms given in an index file and
may be two or three atoms in size.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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>
</TABLE>
<P>
-<HTML>/n<HEAD>/n<TITLE>g_sorient</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_sorient</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_sorient analyzes solvent orientation around solutes.
It calculates two angles between the vector from one or more
reference positions to the first atom of each solvent molecule:<br>theta1: the angle with the vector from the first atom of the solvent
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_tcaf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_tcaf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_tcaf computes tranverse current autocorrelations.
These are used to estimate the shear viscosity eta.
For details see: Palmer, JCP 49 (1994) pp 359-366.<p>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_traj</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_traj</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
g_traj plots coordinates, velocities, forces and/or the box.
With <tt>-com</tt> the coordinates, velocities and forces are
calculated for the center of mass of each group.
When <tt>-mol</tt> is set, the numbers in the index file are
interpreted as molecule numbers and the same procedure as with
<tt>-com</tt> is used for each molecule.<p>
-Option <tt>-ot</tt> plots the temperature of each group.
-This implies <tt>-com</tt>.<p>
-Option <tt>-ekr</tt> plots the rotational kinetic energy of each group.
+Option <tt>-ot</tt> plots the temperature of each group,
+provided velocities are present in the trajectory file.This implies <tt>-com</tt>.<p>
+Option <tt>-ekr</tt> plots the rotational kinetic energy of each group,
+provided velocities are present in the trajectory file.
This implies <tt>-com</tt>.
<P>
<H3>Files</H3>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>
-<HTML>/n<HEAD>/n<TITLE>g_velacc</TITLE>
+<HTML>
+<HEAD>
+<TITLE>g_velacc</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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
function is calculated.<p>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</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]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>-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>-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): 0, 1, 2 or 3 </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: none, exp, aexp, exp_exp or vac </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> or <tt>vac</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>
-<HTML>/n<HEAD>/n<TITLE>genbox</TITLE>
+<HTML>
+<HEAD>
+<TITLE>genbox</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Genbox can do one of 3 things:<p>
1) Generate a box of solvent. Specify -cs and -box. Or specify -cs and
-cp with a structure file with a box, but without atoms.<p>
<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>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>Molecules must be whole in the initial configurations.
<LI>At the moment -ci only works when inserting one molecule.
-<HTML>/n<HEAD>/n<TITLE>genconf</TITLE>
+<HTML>
+<HEAD>
+<TITLE>genconf</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
genconf multiplies a given coordinate file by simply stacking them
on <a href="top.html">top</a> of each other, like a small child playing with wooden blocks.
The program makes a grid of <it>user defined</it>
<TR><TD ALIGN=RIGHT> <b><tt>-[no]renumber</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Renumber residues </TD></TD>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>The program should allow for random displacement off lattice points.
</UL>
-<HTML>/n<HEAD>/n<TITLE>genion</TITLE>
+<HTML>
+<HEAD>
+<TITLE>genion</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
genion replaces solvent molecules by monoatomic ions at
the position of the first atoms with the most favorable electrostatic
potential or at random. The potential is calculated on all atoms, using
-<HTML>/n<HEAD>/n<TITLE>genpr</TITLE>
+<HTML>
+<HEAD>
+<TITLE>genpr</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
genpr 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
-<HTML>/n<HEAD>/n<TITLE>gmxcheck</TITLE>
+<HTML>
+<HEAD>
+<TITLE>gmxcheck</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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>)
and prints out useful information about them.<p>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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>-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>
-<HTML>/n<HEAD>/n<TITLE>gmxdump</TITLE>
+<HTML>
+<HEAD>
+<TITLE>gmxdump</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
gmxdump reads a run input file (<tt>.<a href="tpa.html">tpa</a></tt>/<tt>.<a href="tpr.html">tpr</a></tt>/<tt>.<a href="tpb.html">tpb</a></tt>),
a trajectory (<tt>.<a href="trj.html">trj</a></tt>/<tt>.<a href="trr.html">trr</a></tt>/<tt>.<a href="xtc.html">xtc</a></tt>) or an energy
file (<tt>.<a href="ene.html">ene</a></tt>/<tt>.<a href="edr.html">edr</a></tt>) and prints that to standard
-<HTML>/n<HEAD>/n<TITLE>grompp</TITLE>
+<HTML>
+<HEAD>
+<TITLE>grompp</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
The gromacs preprocessor
reads a molecular topology file, checks the validity of the
file, expands the topology from a molecular description to an atomic
-<HTML>/n<HEAD>/n<TITLE>highway</TITLE>
+<HTML>
+<HEAD>
+<TITLE>highway</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
highway is the gromacs highway simulator. It is an X-windows
gadget that shows a (periodic) autobahn with a user defined
number of cars. Fog can be turned on or off to increase the
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
<hr>
-<HTML>/n<HEAD>/n<TITLE>make_ndx</TITLE>
+<HTML>
+<HEAD>
+<TITLE>make_ndx</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
Index groups are necessary for almost every gromacs program.
All these programs can generate default index groups. You ONLY
have to use make_<a href="ndx.html">ndx</a> when you need SPECIAL index groups.
-<HTML>/n<HEAD>/n<TITLE>mdrun</TITLE>
+<HTML>
+<HEAD>
+<TITLE>mdrun</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
The mdrun program performs Molecular Dynamics simulations.
It reads the run input file (<tt>-s</tt>) and distributes the
topology over nodes if needed. The coordinates are passed
<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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>-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>-[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>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>mk_angndx</TITLE>
+<HTML>
+<HEAD>
+<TITLE>mk_angndx</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
mk_angndx makes an index file for calculation of
angle distributions etc. It uses a run input file (<tt>.tpx</tt>) for the
definitions of the angles, dihedrals etc.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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: angle, <a href="g96.html">g96</a>-angle, dihedral, improper, ryckaert-bellemans or phi-psi </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>
</TABLE>
<P>
<hr>
-<HTML>/n<HEAD>/n<TITLE>ngmx</TITLE>
+<HTML>
+<HEAD>
+<TITLE>ngmx</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>ngmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>ngmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
ngmx is the Gromacs trajectory viewer. This program reads a
trajectory file, a run input file and an index file and plots a
3D structure of your molecule on your standard X Window
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>Balls option does not work
<LI>Some times dumps core without a good reason
-<HTML>/n<HEAD>/n<TITLE>nmrun</TITLE>
+<HTML>
+<HEAD>
+<TITLE>nmrun</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>nmrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>nmrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
nmrun builds a Hessian matrix from single conformation.
For usual Normal Modes-like calculations, make sure that
the structure provided is properly energy-minimised.
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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>-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>-[no]v</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Verbose mode </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>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>pdb2gmx</TITLE>
+<HTML>
+<HEAD>
+<TITLE>pdb2gmx</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
This program reads a <a href="pdb.html">pdb</a> file, lets you choose a forcefield, reads
some database files, adds hydrogens to the molecules and generates
coordinates in Gromacs (Gromos) format and a topology in Gromacs format.
<TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use 1-4 interactions between hydrogen atoms </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]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>-dummy</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to dummy atoms: none, hydrogens or aromatics </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dummy</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Convert atoms to dummy atoms: <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>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>protonate</TITLE>
+<HTML>
+<HEAD>
+<TITLE>protonate</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
<tt>protonate</tt> reads (a) conformation(s) and adds all missing
hydrogens as defined in <tt>ffgmx2.<a href="hdb.html">hdb</a></tt>. If only <tt>-s</tt> is
specified, this conformation will be protonated, if also <tt>-f</tt>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
<hr>
-<HTML>/n<HEAD>/n<TITLE>tpbconv</TITLE>
+<HTML>
+<HEAD>
+<TITLE>tpbconv</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
tpbconv can edit run input files in two ways.<p><b>1st.</b> 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.
-<HTML>/n<HEAD>/n<TITLE>trjcat</TITLE>
+<HTML>
+<HEAD>
+<TITLE>trjcat</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
trjcat concatenates several input trajectory files in sorted order.
In case of double time frames the one in the later file is used.
By specifying <tt>-settime</tt> you will be asked for the start time
-<HTML>/n<HEAD>/n<TITLE>trjconv</TITLE>
+<HTML>
+<HEAD>
+<TITLE>trjconv</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</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>
<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> -1</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> -1</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: ps, fs, ns, us, ms, s, m or h </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>-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: none, whole, inbox or nojump </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: rect, tric or compact </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: <tt>none</tt>, <tt>whole</tt>, <tt>inbox</tt> or <tt>nojump</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>-[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>-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>-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>
-<HTML>/n<HEAD>/n<TITLE>trjorder</TITLE>
+<HTML>
+<HEAD>
+<TITLE>trjorder</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
trjorder orders molecules according to the smallest distance
to atoms in a reference group. It will ask for a group of reference
atoms and a group of molecules. For each frame of the trajectory
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </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>
</TABLE>
-<HTML>/n<HEAD>/n<TITLE>wheel</TITLE>
+<HTML>
+<HEAD>
+<TITLE>wheel</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
wheel plots a helical wheel representation of your sequence.The input sequence is in the .<a href="dat.html">dat</a> file where the first line contains
the number of residues and each consecutive line contains a residuename.
<P>
-<HTML>/n<HEAD>/n<TITLE>x2top</TITLE>
+<HTML>
+<HEAD>
+<TITLE>x2top</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
x2top generates a primitive topology from a coordinate file.
The program assumes all hydrogens are present when defining
the hybridization from the atom name and the number of bonds.
<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>
</TABLE>
<P>
-<H3>Diagnostics</H3>
<UL>
<LI>The atom type selection is primitive. Virtually no chemical knowledge is used
<LI>Periodic boundary conditions screw up the bonding
-<HTML>/n<HEAD>/n<TITLE>xmdrun</TITLE>
+<HTML>
+<HEAD>
+<TITLE>xmdrun</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>xmdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>xmdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
xmdrun is the experimental MD program. New features are tested in this
program before being implemented in the default <a href="mdrun.html">mdrun</a>. Currently under
investigation are: polarizibility, glass simulations,
<TR><TD ALIGN=RIGHT> <b><tt>-[no]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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>-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>-[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]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>
-<HTML>/n<HEAD>/n<TITLE>xpm2ps</TITLE>
+<HTML>
+<HEAD>
+<TITLE>xpm2ps</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
xpm2ps makes a beautiful color plot of an XPixelMap file.
Labels and axis can be displayed, when they are supplied
in the correct matrix format.
<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>-title</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>top</tt> </TD><TD> Show title at: <a href="top.html">top</a>, once, ylabel or none </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>-legend</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>both</tt> </TD><TD> Show legend: both, first, second or none </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: first, second or none </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: halves, add, sub, mult or div </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>-bx</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt> 0</tt> </TD><TD> Box x-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> Box 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: no, blue or red </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>
-<HTML>/n<HEAD>/n<TITLE>xrama</TITLE>
+<HTML>
+<HEAD>
+<TITLE>xrama</TITLE>
<LINK rel=stylesheet href="style.css" type="text/css">
<BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
<table WIDTH="800" NOBORDER >
<TR>
<td WIDTH="120" HEIGHT="133">
-<a href="http://www.gromacs.org/"><img SRC="../
gif/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td><td ALIGN=LEFT VALIGN=TOP WIDTH=480><br><br><h2>Online Reference:<br>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+<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=480><br><br><h2>GROMACS Online Reference:<br>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
<TD ALIGN=RIGHT VALIGN=BOTTOM><B>VERSION 3.0<br>
-Mon 11 Jun 2001</B></td></tr></TABLE>
+Thu 5 Jul 2001</B></td></tr></TABLE>
<HR>
<H3>Description</H3>
+<p>
xrama shows a Ramachandran movie, that is, it shows
the Phi/Psi angles as a function of time in an X-Window.<p>Static Phi/Psi plots for printing can be made with <a href="g_rama.html">g_rama</a>.<p>
Some of the more common X command line options can be used:<br>
<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]X</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt> no</tt> </TD><TD> Use dialog box GUI to edit command line options </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> -1</tt> </TD><TD> First frame (fs) 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> -1</tt> </TD><TD> Last frame (fs) 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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (fs) </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 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> -1</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> -1</tt> </TD><TD> Only use frame when t MOD dt = first time (ps) </TD></TD>
</TABLE>
<P>
<hr>
#BUILT_SOURCES = Makefile.@host@
Makefile.@host@: Template.mak Makefile
- cat $< | sed 's,@libdir\@,$(libdir),' | \
+ cat $(srcdir)/Template.mak | sed 's,@libdir\@,$(libdir),' | \
sed 's,@LDFLAGS\@,$(LDFLAGS),' | \
sed 's,@LIBS\@,$(LIBS),' | \
sed 's,@CPPFLAGS\@,$(CPPFLAGS),' | \
sed 's,@host\@,@host@,' >$@
install-data-hook:
- (cd $(DESTDIR)$(templatedir) && test ! -e Makefile && $(LN_S) Makefile.@host@ Makefile)
+ (cd $(DESTDIR)$(templatedir) && test ! -e Makefile && $(LN_S) Makefile.@host@ Makefile ; exit 0)
-CLEANFILES = *~ \\\#*
+CLEANFILES = Makefile.@host@ *~ \\\#*
cat << _EOF_
-----------------------------------------------------------------
-----------------------------------------------------------------
-This is the GROMACS demo. ( This demo takes about 10-15 min. )
+Welcome to the GROMACS demo!
-In this demo we will demonstrate you how to simulate Molecular
+This is a script that takes about 10 min to run.
+
+In this demo we will demonstrate how to simulate Molecular
Dynamics (MD) using the GROMACS software package.
-This demo will perform a complete molecular dynamics (MD) simulation
-of a small peptide in water. The only input file we need to do this is
-a pdb file of this peptide.
+The demo will perform a complete molecular dynamics (MD) simulation
+of a small peptide in water. The only input file we need to do this
+is a pdb file of a small peptide.
-If you have a problem or remark with respect to this demonstration,
+If you have any problems or remarks with respect to this demonstration,
please mail to: gromacs@gromacs.org , or check the resources on
our website http://www.gromacs.org .
-----------------------------------------------------------------
my_dssp_SOURCES = my_dssp.c dsspcore.c
+total_SOURCES = total.f
+
CLEANFILES = *~ \\\#*
/* Command line options */
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,0,NULL,
+ parse_common_args(&argc,argv,0,NFILE,fnm,0,NULL,
asize(desc),desc,0,NULL);
if (ftp2bSet(efTRN,NFILE,fnm)) {
#define NFILE asize(fnm)
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE ,NFILE,fnm,
asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
top=read_top(ftp2fn(efTPX,NFILE,fnm));
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE ,NFILE,fnm,
asize(pa),pa,asize(desc),desc,0,NULL);
top = read_top(ftp2fn(efTPX,NFILE,fnm));
if (MASTER(cr)) {
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_KEEP_ARGS,TRUE,
+ parse_common_args(&argc,argv,PCA_KEEP_ARGS | PCA_BE_NICE ,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL);
print_pargs(stderr,asize(pa),pa);
}
char *infile,*outfile,title[256],buf[32];
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,NPA,pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
asize(desc),desc,0,NULL);
bCenter = bCenter || (rDist > 0) || bAlternate;
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
if (!in || !out)
matrix boxje;
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,asize(desc),
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,asize(desc),
desc,0,NULL);
if (debug) {
fprintf(debug,"nx = %3d, ny = %3d, nz = %3d\n",nx,ny,nz);
char *infile,*outfile,title[256];
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,NPA,pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,NPA,pa,
asize(desc),desc,0,NULL);
infile = ftp2fn(efSTX,NFILE,fnm);
{
static char *desc[] = {
"All GROMACS programs have 6 standard options,",
- "of which 4 are hidden by default:"
+ "of which some are hidden by default:"
};
static char *bugs[] = {
- "If the configuration script found Motif (or Lesstif) on your system, "
- "all GROMACS programs will have an additional option:[BR]"
+ "If the configuration script found Motif or Lesstif on your system, "
+ "you can use the graphical interface (if not, you will get an error):[BR]"
"[TT]-X[tt] bool [TT]no[tt] Use dialog box GUI to edit command line options",
"When compiled on an SGI-IRIX system, all GROMACS programs have an "
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,
+ parse_common_args(&argc,argv,0,
0,NULL,0,NULL,asize(desc),desc,asize(bugs),bugs);
thanx(stderr);
tensor P;
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
/* Read initial topology and coordaintes etc. */
/* CopyRight(stdout,argv[0]);*/
parse_common_args(&argc,argv,PCA_CAN_VIEW,
- FALSE,NFILE,fnm,asize(pa),pa,asize(desc),
+ NFILE,fnm,asize(pa),pa,asize(desc),
desc,0,NULL);
if (opt2parg_bSet("-sig",asize(pa),pa) ||
/* CopyRight(stdout,argv[0]);*/
parse_common_args(&argc,argv,PCA_CAN_VIEW,
- FALSE,NFILE,fnm,asize(pa),pa,asize(desc),
+ NFILE,fnm,asize(pa),pa,asize(desc),
desc,0,NULL);
if (opt2parg_bSet("-sig",asize(pa),pa) ||
mkinl: $(MKINL_OBJ)
$(BUILD_COMPILE) -o $@ $(MKINL_OBJ)
-# link the mpi library to non-mpi names if the latter are not present
+# link the mpi library to non-mpi names if the latter are not present after install
install-exec-hook:
libname="libgmx@LIBSUFFIX@"; nompi="`echo $$libname | sed -e 's,_mpi,,'`";
if test `echo $$libname|grep _mpi`; then \
- (cd $(libdir) && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a); \
- (cd $(libdir) && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so);\
+ (cd $(libdir) && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
+ (cd $(libdir) && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0);\
fi;
+
# clean all libtool libraries, since the target names might have changed
CLEANFILES = *.la *~ \\\#* innerc.c innerf.f mkinl
+
abort();
}
-#ifdef USE_SGI_FPE
+#ifdef __sgi
void doexceptions(void)
{
#include <sigfpe.h>
signal(hs[i],handle_signals);
}
#endif
+
#endif
fflush(fp);
}
-void pr_fopts(FILE *fp,int nf,t_filenm tfn[])
+void pr_fopts(FILE *fp,int nf,t_filenm tfn[], int shell)
{
int i,j;
- for(i=0; (i<nf); i++) {
- fprintf(fp," \"n/%s/f:*.",tfn[i].opt);
- if (deffile[tfn[i].ftp].ntps) {
+ switch (shell) {
+ case eshellCSH:
+ for(i=0; (i<nf); i++) {
+ fprintf(fp," \"n/%s/f:*.",tfn[i].opt);
+ if (deffile[tfn[i].ftp].ntps) {
+ fprintf(fp,"{");
+ for(j=0; j<deffile[tfn[i].ftp].ntps; j++) {
+ if (j>0)
+ fprintf(fp,",");
+ fprintf(fp,"%s",deffile[deffile[tfn[i].ftp].tps[j]].ext+1);
+ }
+ fprintf(fp,"}");
+ } else
+ fprintf(fp,"%s",deffile[tfn[i].ftp].ext+1);
fprintf(fp,"{");
- for(j=0; j<deffile[tfn[i].ftp].ntps; j++) {
+ for(j=0; j<NZEXT; j++)
+ fprintf(fp,",%s",z_ext[j]);
+ fprintf(fp,"}/\"");
+ }
+ break;
+ case eshellBASH:
+ for(i=0; (i<nf); i++) {
+ fprintf(fp,"%s) COMPREPLY=( $(compgen -X '!*.",tfn[i].opt);
+ if (deffile[tfn[i].ftp].ntps) {
+ fprintf(fp,"+(");
+ for(j=0; j<deffile[tfn[i].ftp].ntps; j++) {
+ if (j>0)
+ fprintf(fp,"|");
+ fprintf(fp,"%s",deffile[deffile[tfn[i].ftp].tps[j]].ext+1);
+ }
+ fprintf(fp,")");
+ } else
+ fprintf(fp,"%s",deffile[tfn[i].ftp].ext+1);
+ fprintf(fp,"*(");
+ for(j=0; j<NZEXT; j++) {
if (j>0)
- fprintf(fp,",");
- fprintf(fp,"%s",deffile[deffile[tfn[i].ftp].tps[j]].ext+1);
+ fprintf(fp,"|");
+ fprintf(fp,"%s",z_ext[j]);
}
- fprintf(fp,"}");
- } else
- fprintf(fp,"%s",deffile[tfn[i].ftp].ext+1);
- fprintf(fp,"{");
- for(j=0; j<NZEXT; j++)
- fprintf(fp,",%s",z_ext[j]);
- fprintf(fp,"}/\"");
+ fprintf(fp,")' -f $c ; compgen -S '/' -X '.*' -d $c ));;\n");
+ }
+ break;
+ case eshellZSH:
+ for(i=0; (i<nf); i++) {
+ fprintf(fp,"- 'c[-1,%s]' -g '*.",tfn[i].opt);
+ if (deffile[tfn[i].ftp].ntps) {
+ fprintf(fp,"(");
+ for(j=0; j<deffile[tfn[i].ftp].ntps; j++) {
+ if (j>0)
+ fprintf(fp,"|");
+ fprintf(fp,"%s",deffile[deffile[tfn[i].ftp].tps[j]].ext+1);
+ }
+ fprintf(fp,")");
+ } else
+ fprintf(fp,"%s",deffile[tfn[i].ftp].ext+1);
+ fprintf(fp,"(");
+ for(j=0; j<NZEXT; j++)
+ fprintf(fp,"|%s",z_ext[j]);
+ fprintf(fp,") *(/)' ");
+ }
+ break;
}
}
}
}
-void pr_enums(FILE *fp, int npargs,t_pargs pa[])
+void pr_enums(FILE *fp, int npargs,t_pargs pa[], int shell)
{
int i,j;
-
- for (i=0; i<npargs; i++)
- if (pa[i].type==etENUM) {
- fprintf(fp," \"n/%s/(",pa[i].option);
- for(j=1; pa[i].u.c[j]; j++)
- fprintf(fp," %s",pa[i].u.c[j]);
- fprintf(fp,")/\"");
- }
+
+ switch (shell) {
+ case eshellCSH:
+ for (i=0; i<npargs; i++)
+ if (pa[i].type==etENUM) {
+ fprintf(fp," \"n/%s/(",pa[i].option);
+ for(j=1; pa[i].u.c[j]; j++)
+ fprintf(fp," %s",pa[i].u.c[j]);
+ fprintf(fp,")/\"");
+ }
+ break;
+ case eshellBASH:
+ for (i=0; i<npargs; i++)
+ if (pa[i].type==etENUM) {
+ fprintf(fp,"%s) COMPREPLY=( $(compgen -W '",pa[i].option);
+ for(j=1; pa[i].u.c[j]; j++)
+ fprintf(fp," %s",pa[i].u.c[j]);
+ fprintf(fp," ' -- $c ));;\n");
+ }
+ break;
+ case eshellZSH:
+ for (i=0; i<npargs; i++)
+ if (pa[i].type==etENUM) {
+ fprintf(fp,"- 'c[-1,%s]' -s \"", pa[i].option);
+ for(j=1; pa[i].u.c[j]; j++)
+ fprintf(fp," %s",pa[i].u.c[j]);
+ fprintf(fp,"\" ");
+ }
+ break;
+ }
}
return newdesc;
}
-void parse_common_args(int *argc,char *argv[],unsigned long Flags,bool bNice,
+void parse_common_args(int *argc,char *argv[],unsigned long Flags,
int nfile,t_filenm fnm[],int npargs,t_pargs *pa,
int ndesc,char **desc,int nbugs,char **bugs)
{
t_pargs motif_pa = { "-X", FALSE, etBOOL, {&bGUI},
"Use dialog box GUI to edit command line options" };
- t_pargs fpe_pa = { "-exception", FALSE, etBOOL, {&bExcept},
- "HIDDENTurn on exception handling" };
t_pargs npri_paX = { "-npri", FALSE, etENUM, {not_npristr},
"Set non blocking priority" };
t_pargs npri_pa = { "-npri", FALSE, etINT, {&npri},
- "Set non blocking priority (try 128)" };
+ "HIDDEN Set non blocking priority (try 128)" };
t_pargs nice_paX = { "-nice", FALSE, etENUM, {not_nicestr},
"Set the nicelevel" };
t_pargs nice_pa = { "-nice", FALSE, etINT, {&nicelevel},
}
if (bGUI)
bQuiet = TRUE;
+#else
+ bGUI = FALSE;
#endif
/* When you run a dynamically linked program before installing
npall = add_parg(npall,&(all_pa),&(pca_pa[i]));
/* Motif options */
-#ifdef HAVE_MOTIF
npall = add_parg(npall,&(all_pa),&motif_pa);
-#endif
#ifdef __sgi
-#ifdef USE_SGI_FPE
- npall = add_parg(npall,&(all_pa),&fpe_pa);
-#endif
-#ifndef NO_NICE
+ bExcept = (getenv("GMXSGIFPE") != NULL);
+
envstr = getenv("GMXNPRIALL");
if (envstr)
npri=atoi(envstr);
- if (FF(PCA_SET_NPRI)) {
+ if (FF(PCA_BE_NICE)) {
envstr = getenv("GMXNPRI");
if (envstr)
npri=atoi(envstr);
else
npall = add_parg(npall,&(all_pa),&npri_pa);
#endif
-#endif
-#ifndef NO_NICE
if (bGUI) {
/* Automatic nice or scheduling options */
- if (bNice)
+ if (FF(PCA_BE_NICE))
nice_paX.u.c = nicestr;
npall = add_parg(npall,&(all_pa),&nice_paX);
}
else {
- if (bNice)
+ if (FF(PCA_BE_NICE))
nicelevel=19;
npall = add_parg(npall,&(all_pa),&nice_pa);
}
-#endif
if (FF(PCA_CAN_SET_DEFFNM))
npall = add_parg(npall,&(all_pa),&deffnm_pa);
buf,__FILE__,__LINE__);
}
-#ifdef HAVE_MOTIF
/* Now we have parsed the command line arguments. If the user wants it
* we can now plop up a GUI dialog box to edit options.
*/
if (bGUI) {
+#ifdef HAVE_MOTIF
gmx_gui(argc,argv,nfile,fnm,npall,all_pa,ndesc,desc,nbugs,bugs);
- }
+#else
+ fatal_error(0,"GROMACS compiled without MOTIF support - can't use X interface");
#endif
+ }
/* Now copy the results back... */
for(i=0,k=npall-npargs; (i<npargs); i++,k++)
bExit = bHelp || (strcmp(manstr[0],"no") != 0);
#ifdef __sgi
-#ifdef USE_SGI_FPE
/* Install exception handler if necessary */
if (bExcept)
doexceptions();
#endif
-#endif
-
+
/* Set the nice level */
#ifdef __sgi
if (bGUI)
(void) schedctl(MPTS_RTPRI,0,npri);
}
else
-#endif
-#ifndef NO_NICE
+#endif
+
+#ifdef HAVE_UNISTD_H
if (bGUI) {
- if (bNice)
+ if (FF(PCA_BE_NICE))
sscanf(nicestr[0],"%d",&nicelevel);
else
sscanf(not_nicestr[0],"%d",&nicelevel);
}
if (nicelevel != 0 && !bExit)
nice(nicelevel);
-
#endif
if (!(FF(PCA_QUIET) || bQuiet )) {
}
if (strcmp(manstr[0],"no") != 0) {
- fp=man_file(program,manstr[0]);
- write_man(fp,manstr[0],program,ndesc,desc,nfile,fnm,npall,all_pa,
- nbugs,bugs,bHidden);
- fclose(fp);
+ if(!strcmp(manstr[0],"completion")) {
+ /* one file each for csh, bash and zsh if we do completions */
+ fp=man_file(program,"completion-zsh");
+ write_man(fp,"completion-zsh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
+ fclose(fp);
+ fp=man_file(program,"completion-bash");
+ write_man(fp,"completion-bash",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
+ fclose(fp);
+ fp=man_file(program,"completion-csh");
+ write_man(fp,"completion-csh",program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
+ fclose(fp);
+ } else {
+ fp=man_file(program,manstr[0]);
+ write_man(fp,manstr[0],program,ndesc,desc,nfile,fnm,npall,all_pa,nbugs,bugs,bHidden);
+ fclose(fp);
+ }
}
/* convert time options, must be done after printing! */
static void pr_opts(FILE *fp,
int nfile, t_filenm *fnm,
- int npargs, t_pargs pa[])
+ int npargs, t_pargs pa[], int shell)
{
int i;
- fprintf(fp," \"c/-/(");
- for (i=0; i<nfile; i++)
- fprintf(fp," %s",fnm[i].opt+1);
- for (i=0; i<npargs; i++)
- if ( (pa[i].type==etBOOL) && *(pa[i].u.b) )
- fprintf(fp," no%s",pa[i].option+1);
- else
- fprintf(fp," %s",pa[i].option+1);
- fprintf(fp,")/\"");
-
+ switch (shell) {
+ case eshellCSH:
+ fprintf(fp," \"c/-/(");
+ for (i=0; i<nfile; i++)
+ fprintf(fp," %s",fnm[i].opt+1);
+ for (i=0; i<npargs; i++)
+ if ( (pa[i].type==etBOOL) && *(pa[i].u.b) )
+ fprintf(fp," no%s",pa[i].option+1);
+ else
+ fprintf(fp," %s",pa[i].option+1);
+ fprintf(fp,")/\"");
+ break;
+ case eshellBASH:
+ fprintf(fp,"if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen -W '");
+ for (i=0; i<nfile; i++)
+ fprintf(fp," -%s",fnm[i].opt+1);
+ for (i=0; i<npargs; i++)
+ if ( (pa[i].type==etBOOL) && *(pa[i].u.b) )
+ fprintf(fp," -no%s",pa[i].option+1);
+ else
+ fprintf(fp," -%s",pa[i].option+1);
+ fprintf(fp,"' -- $c)); return 0; fi\n");
+ break;
+ case eshellZSH:
+ fprintf(fp," -x 's[-]' -s \"");
+ for (i=0; i<nfile; i++)
+ fprintf(fp," %s",fnm[i].opt+1);
+ for (i=0; i<npargs; i++)
+ if ( (pa[i].type==etBOOL) && *(pa[i].u.b) )
+ fprintf(fp," no%s",pa[i].option+1);
+ else
+ fprintf(fp," %s",pa[i].option+1);
+ fprintf(fp,"\" ");
+ break;
+ }
}
-static void write_compl(FILE *out,
- int nfile, t_filenm *fnm,
- int npargs, t_pargs *pa)
+static void write_cshcompl(FILE *out,
+ int nfile, t_filenm *fnm,
+ int npargs, t_pargs *pa)
{
fprintf(out,"complete %s",ShortProgram());
- pr_enums(out,npargs,pa);
- pr_fopts(out,nfile,fnm);
- pr_opts(out,nfile,fnm,npargs,pa);
+ pr_enums(out,npargs,pa,eshellCSH);
+ pr_fopts(out,nfile,fnm,eshellCSH);
+ pr_opts(out,nfile,fnm,npargs,pa,eshellCSH);
fprintf(out,"\n");
}
+static void write_zshcompl(FILE *out,
+ int nfile, t_filenm *fnm,
+ int npargs, t_pargs *pa)
+{
+ fprintf(out,"compctl ");
+
+ /* start with options, since they are always present */
+ pr_opts(out,nfile,fnm,npargs,pa,eshellZSH);
+ pr_enums(out,npargs,pa,eshellZSH);
+ pr_fopts(out,nfile,fnm,eshellZSH);
+ fprintf(out,"-- %s\n",ShortProgram());
+}
+
+static void write_bashcompl(FILE *out,
+ int nfile, t_filenm *fnm,
+ int npargs, t_pargs *pa)
+{
+ /* Advanced bash completions are handled by shell functions.
+ * p and c hold the previous and current word on the command line.
+ * We need to use extended globbing, so write it in each completion file */
+ fprintf(out,"shopt -s extglob\n");
+ fprintf(out,"_%s_compl() {\nlocal p c\n",ShortProgram());
+ fprintf(out,"COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}\n");
+ pr_opts(out,nfile,fnm,npargs,pa,eshellBASH);
+ fprintf(out,"case \"$p\" in\n");
+ pr_enums(out,npargs,pa,eshellBASH);
+ pr_fopts(out,nfile,fnm,eshellBASH);
+ fprintf(out,"esac }\ncomplete -F _%s_compl %s\n",ShortProgram(),ShortProgram());
+}
+
void write_man(FILE *out,char *mantp,
char *program,
int nldesc,char **desc,
char *pr;
int i,npar;
t_pargs *par;
- bool bCopy;
-
- bCopy = !(bHidden || (strcmp(mantp,"completion")==0) );
- if (!bCopy) {
+
+ /* Don't write hidden options to completions, it just
+ * makes the options more complicated for normal users
+ */
+
+ if (bHidden) {
npar=npargs;
par=pa;
}
write_htmlman(out,pr,nldesc,desc,nfile,fnm,npar,par,nbug,bugs);
if (strcmp(mantp,"java")==0)
write_java(out,pr,nldesc,desc,nfile,fnm,npar,par,nbug,bugs);
- if (strcmp(mantp,"completion")==0)
- write_compl(out,nfile,fnm,npar,par);
+ if (strcmp(mantp,"completion-zsh")==0)
+ write_zshcompl(out,nfile,fnm,npar,par);
+ if (strcmp(mantp,"completion-bash")==0)
+ write_bashcompl(out,nfile,fnm,npar,par);
+ if (strcmp(mantp,"completion-csh")==0)
+ write_cshcompl(out,nfile,fnm,npar,par);
- if (bCopy)
+ if (!bHidden)
sfree(par);
}
protonate nmrun luck gmxdump \
gmxcheck x2top xmdrun
+EXTRA_dist = mdrun.1
+
+mdrun.1:
+ cp mdrun.c mdrun.1
+ touch mdrun.1
grompp_SOURCES = \
};
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
fn1 = opt2fn_null("-f",NFILE,fnm);
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
pr_shownumbers(bShowNumbers);
init_ir(ir,opts);
/* Parse the command line */
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
if ((nnodes > 0) && (nnodes <= MAXNODES))
/* Command line options ! */
static bool bVerbose = FALSE;
static bool bCompact = TRUE;
- static bool bLateVir = TRUE;
- static bool bTweak = FALSE;
static bool bSepDVDL = FALSE;
+
+ /* static bool bLateVir = TRUE; */
+ /* static bool bTweak = FALSE; */
+ static int nDLB=0;
+
#ifdef XMDRUN
static bool bMultiSim = FALSE;
static bool bGlas = FALSE;
static bool bIonize = FALSE;
#endif
-#ifdef USE_MPI
static int nnodes=1;
-#endif
- static int nDLB=0,nstepout=10;
+ static int nstepout=10;
static t_pargs pa[] = {
-#ifdef USE_MPI
{ "-np", FALSE, etINT, {&nnodes},
"Number of nodes, must be the same as used for grompp" },
-#endif
{ "-v", FALSE, etBOOL,{&bVerbose}, "Be loud and noisy" },
{ "-compact", FALSE, etBOOL,{&bCompact}, "Write a compact log file" },
#ifdef XMDRUN
"Do a simulation including the effect of an X-Ray bombardment on your system" },
#endif
{ "-sepdvdl", FALSE, etBOOL,{&bSepDVDL},
- "HIDDENWrite separate V and dVdl terms for each interaction type and each node(!) to log file(s)" },
- { "-latevir", FALSE, etBOOL,{&bLateVir},
- "HIDDENCalculate virial late in the algorithm" },
- { "-tweak", FALSE, etBOOL,{&bTweak},
- "HIDDENModify PME virial computation" },
- { "-dlb", FALSE, etINT, {&nDLB},
- "HIDDENUse dynamic load balancing every ... step. BUGGY do not use" },
+ "HIDDENWrite separate V and dVdl terms for each interaction and node(!) to log file(s)" },
+ /* { "-latevir", FALSE, etBOOL,{&bLateVir},
+ "HIDDENCalculate virial late in the algorithm" }, */
+ /* { "-tweak", FALSE, etBOOL,{&bTweak},
+ "HIDDENModify PME virial computation" }, */
+ /* { "-dlb", FALSE, etINT, {&nDLB},
+ "HIDDENUse dynamic load balancing every ... step. BUGGY do not use" }, */
{ "-stepout", FALSE, etINT, {&nstepout},
"HIDDENFrequency of writing the remaining runtime" }
};
t_edsamyn edyn;
unsigned long Flags;
-
+
cr = init_par(&argc,&argv);
bVerbose = bVerbose && MASTER(cr);
edyn.bEdsam=FALSE;
+
if (MASTER(cr))
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,
- PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_SET_NPRI |
+ PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_BE_NICE |
PCA_CAN_SET_DEFFNM | (MASTER(cr) ? 0 : PCA_QUIET),
- TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+#ifndef USE_MPI
+ if (nnodes>1)
+ fatal_error(0,"GROMACS compiled without MPI support - can't do parallel runs");
+#endif
+
open_log(ftp2fn(efLOG,NFILE,fnm),cr);
#ifdef XMDRUN
ed_open(NFILE,fnm,&edyn);
Flags = opt2bSet("-rerun",NFILE,fnm) ? MD_RERUN : 0;
- Flags = Flags | (bLateVir ? MD_LATEVIR : 0);
- Flags = Flags | (bTweak ? MD_TWEAK : 0);
+ /* Flags = Flags | (bLateVir ? MD_LATEVIR : 0); */
+ /* Flags = Flags | (bTweak ? MD_TWEAK : 0); */
Flags = Flags | (bSepDVDL ? MD_SEPDVDL : 0);
#ifdef XMDRUN
/* Command line options ! */
static bool bVerbose=FALSE,bCompact=TRUE;
-#ifdef USE_MPI
static int nnodes=1;
-#endif
static int nDLB=0,nstepout=10;
static t_pargs pa[] = {
-#ifdef USE_MPI
{ "-np", FALSE, etINT, {&nnodes},
"Number of nodes, must be the same as used for grompp" },
-#endif
{ "-v", FALSE, etBOOL,{&bVerbose}, "Verbose mode" },
{ "-compact", FALSE, etBOOL,{&bCompact},
"Write a compact log file" },
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,
- PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_SET_NPRI |
+ PCA_KEEP_ARGS | PCA_NOEXIT_ON_ARGS | PCA_BE_NICE |
(MASTER(cr) ? 0 : PCA_QUIET),
- TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+
+#ifndef USE_MPI
+ if (nnodes>1)
+ fatal_error(0,"GROMACS compiled without MPI support - can't do parallel runs");
+#endif
open_log(ftp2fn(efLOG,NFILE,fnm),cr);
#define NPARGS asize(pa)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
if (bInter) {
/* if anything changes here, also change description of -inter */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,FALSE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL);
infile=opt2fn("-s",NFILE,fnm);
#include <string.h>
#include <errno.h>
#include <ctype.h>
-
+#include "futil.h"
#include "assert.h"
#include "sysstuff.h"
#include "typedefs.h"
static int bFirst=1;
if(bFirst) {
- if((lib=getenv("GMXLIB")) != NULL)
+ lib=getenv("GMXLIB");
+ if(lib!=NULL) {
strcpy(libdir,lib);
- else
- strcpy(libdir,GMXLIBDIR);
+ } else {
+ if(get_libdir(libdir))
+ strcpy(libdir,GMXLIBDIR);
+ }
bFirst=0;
}
-
/* build the command line */
sprintf(command,"%s %s -I%s %s %s %s",
int *nsim,
t_simsystem **sims)
{
- char tmpfile[L_tmpnam];
+ char tmpfile[13];
char **title;
int combination_rule;
CopyRight(stdout,argv[0]);
/* Parse the command line */
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
bTime = opt2parg_bSet("-time",asize(pa),pa);
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,asize(bugs),bugs);
bRTP = opt2bSet("-r",NFILE,fnm);
bTOP = opt2bSet("-r",NFILE,fnm);
libmd@LIBSUFFIX@_la_LIBADD = @MDLIB_LIBOBJS@
libmd@LIBSUFFIX@_la_DEPENDENCIES = @MDLIB_LIBOBJS@
+libmd@LIBSUFFIX@_la_LDFLAGS = -version-info @SHARED_VERSION_INFO@
lib_LTLIBRARIES = libmd@LIBSUFFIX@.la
install-exec-hook:
libname="libmd@LIBSUFFIX@"; nompi="`echo $$libname | sed -e 's,_mpi,,'`";
if test `echo $$libname|grep _mpi`; then \
- (cd $(libdir) && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a); \
- (cd $(libdir) && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so);\
+ (cd $(libdir) && test -e $$libname.a -a ! -e $$nompi.a && $(LN_S) $$libname.a $$nompi.a ; exit 0); \
+ (cd $(libdir) && test -e $$libname.so -a ! -e $$nompi.so && $(LN_S) $$libname.so $$nompi.so ; exit 0);\
fi;
+
# clean all libtool libraries, since the target names might have changed
CLEANFILES = *.la *~ \\\#*
-
-
-
-
#define NFILE asize(fnm)
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,FALSE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,
0,NULL,asize(desc),desc,0,NULL);
if ((x11=GetX11(&argc,argv))==NULL) {
#define NFILE asize(fnm)
CopyRight(stdout,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,FALSE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,
0,NULL,asize(desc),desc,asize(bugs),bugs);
if ((x11=GetX11(&argc,argv))==NULL) {
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,FALSE,NFILE,fnm,0,NULL,
+ parse_common_args(&argc,argv,PCA_CAN_TIME,NFILE,fnm,0,NULL,
asize(desc),desc,0,NULL);
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
#ifndef DOUBLE
if (MASTER(cr)) {
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,
+ parse_common_args(&argc,argv,PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
/* Copy arguments to correct structure */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT,
- TRUE, NFILE,fnm, asize(pa),pa, asize(desc),desc,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE ,
+ NFILE,fnm, asize(pa),pa, asize(desc),desc,
#ifdef MY_DSSP
0,NULL
#else
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW,FALSE,NFILE,fnm,NPA,pa,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW,NFILE,fnm,NPA,pa,
asize(desc),desc,asize(bugs),bugs);
bIndex = opt2bSet("-n",NFILE,fnm) || bNDEF;
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS,TRUE,
+ parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS | PCA_BE_NICE ,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
tadjust=0;
snew(fnms,argc);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- TRUE,NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE ,
+ NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
indexfile=ftp2fn_null(efNDX,NFILE,fnm);
ppa = add_acf_pargs(&npargs,pa);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_BE_NICE ,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
acfile = opt2fn_null("-ac",NFILE,fnm);
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs);
mult = 4;
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE ,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&gnx,&index,&grpname);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&xtop,NULL,box,TRUE);
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,asize(bugs),bugs);
/* Handle result from enumerated type */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* parse options */
bReadMat = opt2bSet("-dm",NFILE,fnm);
bool bHaveV,bReadV;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,NFILE,fnm,
0,NULL,asize(desc),desc,0,NULL);
ftpout=fn2ftp(ftp2fn(efTRX,NFILE,fnm));
bHaveV=((ftpout==efTRJ) || (ftpout==efTRR));
real rms;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,
+ parse_common_args(&argc,argv,PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
/* reading reference structure from first structure file */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_SET_NPRI,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
clear_mat(zerobox);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
/* Calculate axis */
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
please_cite(stdout,"Spoel98a");
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
if (mult != -1)
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
printf("Using %g as mu_max and %g as the dipole moment.\n",
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
init5(ntop);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
bCutoff=opt2parg_bSet("-dist",NPA,pa);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
get_stx_coordnum (opt2fn("-f",NFILE,fnm),&natoms);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
egrp_use[egCOUL]=bCoul;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_BEGIN | PCA_CAN_END | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
bDRAll = opt2bSet("-pairs",NFILE,fnm);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
clear_rvec(d);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, TRUE, NFILE,
+ parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE, NFILE,
fnm, asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
bMicel = opt2bSet("-nm",NFILE,fnm);
real **rhbex;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
/* process input */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
bRange=(opt2parg_bSet("-ahxstart",asize(pa),pa) &&
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
fp = open_enx(ftp2fn(efENX,NFILE,fnm),"r");
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,NFILE,fnm,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,NFILE,fnm,
asize(pa),pa,asize(desc),desc,0,NULL);
fprintf(stderr,"Will truncate at %f nm\n",truncate);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
tps = ftp2fn_null(efTPS,NFILE,fnm);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,PCA_CAN_VIEW,
- FALSE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
get_stx_coordnum (opt2fn("-f1",NFILE,fnm),&nat1);
get_stx_coordnum (opt2fn("-f2",NFILE,fnm),&nat2);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT,
- TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
trx_file = ftp2fn_null(efTRX,NFILE,fnm);
tps_file = ftp2fn_null(efTPS,NFILE,fnm);
ndx_file = ftp2fn_null(efNDX,NFILE,fnm);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
do_multipoles(ftp2fn(efTRX,NFILE,fnm),ftp2fn(efTPX,NFILE,fnm),
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_SET_NPRI,TRUE,
+ parse_common_args(&argc,argv,PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&top_x,NULL,box,bM);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,
+ parse_common_args(&argc,argv,PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
indexfile=ftp2fn_null(efNDX,NFILE,fnm);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0, NULL);
/* Calculate axis */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME, TRUE,
+ parse_common_args(&argc, argv, PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,asize(bugs),bugs);
/* Calculate axis */
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL);
int g,ng,natoms,i,j,k,nbin,j0,j1,n,nframes;
int **count;
char **grpname;
- int *isize,isize_cm,nrdf,max_i;
- atom_id **index,*index_cm;
+ int *isize,isize_cm=0,nrdf=0,max_i;
+ atom_id **index,*index_cm=NULL;
unsigned long int *sum;
real t,boxmin,hbox,hbox2,cut2,r,r2,invbinw,normfac;
real segvol,spherevol,prev_spherevol,**rdf;
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,NPA,pa,asize(desc),desc,0,NULL);
fnTPS = ftp2fn_null(efTPS,NFILE,fnm);
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (taum <= 0)
fatal_error(0,"Please give me a sensible taum!\n");
int i,j,k,m,n,teller,teller2,tel_mat,tel_mat2;
#define NFRAME 5000
int maxframe=NFRAME,maxframe2=NFRAME;
- real t,lambda,*w_rls,*w_rms,tmas,*w_rls_m,*w_rms_m;
+ real t,lambda,*w_rls,*w_rms,tmas,*w_rls_m=NULL,*w_rms_m=NULL;
bool bTruncOct,bNorm,bAv,bFreq2,bFile2,bMat,bBond,bDelta,bMirror;
t_topology top;
int nrms,ncons=0;
FILE *fp;
- real rlstot=0,**rls,**rlsm,*time,*time2,*rlsnorm=NULL,**rmsd_mat=NULL,
+ real rlstot=0,**rls,**rlsm=NULL,*time,*time2,*rlsnorm=NULL,**rmsd_mat=NULL,
**bond_mat=NULL,
*axis,*axis2,*del_xaxis,*del_yaxis,
rmsd_max,rmsd_min,rmsd_avg,bond_max,bond_min,ang,ipr;
real **rmsdav_mat=NULL,av_tot,weight,weight_tot;
real **delta=NULL,delta_max,delta_scalex=0,delta_scaley=0,*delta_tot;
int delta_xsize=0,del_lev=100,mx,my,abs_my;
- bool bA1,bA2,bPrev,bTop,*bInMat;
- int ifit,*irms,ibond=0,*ind_bond=NULL,n_ind_m;
- atom_id *ind_fit,**ind_rms,*ind_m,*rev_ind_m,*ind_rms_m;
+ bool bA1,bA2,bPrev,bTop,*bInMat=NULL;
+ int ifit,*irms,ibond=0,*ind_bond=NULL,n_ind_m=0;
+ atom_id *ind_fit,**ind_rms,*ind_m=NULL,*rev_ind_m,*ind_rms_m=NULL;
char *gn_fit,**gn_rms;
t_rgb rlo,rhi;
t_filenm fnm[] = {
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW,
- TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_TIME_UNIT | PCA_CAN_VIEW | PCA_BE_NICE,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
ewhat=nenum(what);
if (ewhat==ewRho || ewhat==ewRhoSc)
please_cite(stdout,"Maiorov95");
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE ,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
bRMS = opt2bSet("-rms", NFILE,fnm);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE ,
NFILE,fnm,asize(pargs),pargs,asize(desc),desc,0,NULL);
bReadPDB = ftp2bSet(efPDB,NFILE,fnm);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
rd_index(ftp2fn(efNDX,NFILE,fnm),1,&isize,&index,&grpname);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
snew(x,run_time+1);
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
top=read_top(ftp2fn(efTPX,NFILE,fnm));
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (solsize <= 0) {
solsize=1e-3;
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,0,NULL,asize(desc),desc,0,NULL);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
two_pi = 2/M_PI;
char *fn_tca,char *fn_tc,char *fn_tcf,char *fn_cub,
char *fn_vk)
{
- FILE *fp,*fp_vk,*fp_cub;
+ FILE *fp,*fp_vk,*fp_cub=NULL;
int nk,ntc;
- real **tcaf,**tcafc,eta;
+ real **tcaf,**tcafc=NULL,eta;
int i,j,k,kc;
int ncorr;
real fitparms[3],*sig;
matrix box;
bool bTPS,bTop; /* ,bCubic; */
int gnx;
- atom_id *index,*a,*atndx,at;
+ atom_id *index,*a=NULL,*atndx=NULL,at;
char *grpname;
char title[256];
real t0,t1,dt,m,mtot,sysmass,rho,sx,cx;
CopyRight(stderr,argv[0]);
npargs = asize(pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,pa,asize(desc),desc,0,NULL);
bTop=read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,NULL,NULL,box,TRUE);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
if (bMol)
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW | PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
bTPS = bMol || ftp2bSet(efTPS,NFILE,fnm) || !ftp2bSet(efNDX,NFILE,fnm);
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv, PCA_BE_NICE,NFILE,fnm,asize(pa),pa,
asize(desc),desc,asize(bugs),bugs);
bInsert = opt2bSet("-ci",NFILE,fnm) && (nmol_ins > 0);
};
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,asize(bugs),bugs);
bTRX = ftp2bSet(efTRX,NFILE,fnm);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
fprintf(stderr,"Will subtract %d from res numbers in %s\n",
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ parse_common_args(&argc,argv,PCA_BE_NICE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
bPDB = ftp2bSet(efPDB,NFILE,fnm);
if (bRandom && bPDB) {
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
if ( !ftp2bSet(efNDX,NFILE,fnm) ) {
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,0,NULL,asize(desc),
+ parse_common_args(&argc,argv,0,NFILE,fnm,0,NULL,asize(desc),
desc,0,NULL);
get_stx_coordnum(ftp2fn(efSTX,NFILE,fnm),&(atoms.nr));
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,FALSE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,0,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
bPP = FALSE;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ parse_common_args(&argc,argv,PCA_BE_NICE,NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
snew(ss,nres);
CopyRight(stderr,argv[0]);
npargs = asize(pa);
ppa = add_acf_pargs(&npargs,pa);
- parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_CAN_VIEW | PCA_BE_NICE,
NFILE,fnm,npargs,ppa,asize(desc),desc,0,NULL);
snew(data,nframes);
snew(data2,nframes);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS,TRUE,
+ parse_common_args(&argc,argv,PCA_NOEXIT_ON_ARGS | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
CopyRight(stderr,argv[0]);
parse_common_args(&argc,argv,
- PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT,
- TRUE, NFILE,fnm,asize(pa),pa,asize(desc),desc,
+ PCA_CAN_BEGIN | PCA_CAN_END | PCA_CAN_VIEW | PCA_TIME_UNIT | PCA_BE_NICE,
+ NFILE,fnm,asize(pa),pa,asize(desc),desc,
0,NULL);
top_file=ftp2fn(efTPS,NFILE,fnm);
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_TIME,TRUE,
+ parse_common_args(&argc,argv,PCA_CAN_TIME | PCA_BE_NICE,
NFILE,fnm,asize(pa),pa,asize(desc),desc,0,NULL);
read_tps_conf(ftp2fn(efTPS,NFILE,fnm),title,&top,&x,NULL,box,TRUE);
char **resnm;
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,0,TRUE,NFILE,fnm,asize(pa),pa,
+ parse_common_args(&argc,argv,PCA_BE_NICE,NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
for(i=1; (i<argc); i++) {
#define NFILE asize(fnm)
CopyRight(stderr,argv[0]);
- parse_common_args(&argc,argv,PCA_CAN_VIEW,FALSE,
+ parse_common_args(&argc,argv,PCA_CAN_VIEW,
NFILE,fnm,asize(pa),pa,
asize(desc),desc,0,NULL);
epsfile=ftp2fn_null(efEPS,NFILE,fnm);
xpmfile=opt2fn_null("-xpm",NFILE,fnm);
- if ( epsfile==NULL && xpmfile==NULL )
+ if ( epsfile==NULL && xpmfile==NULL ) {
if (ecombine!=ecHalves)
xpmfile=opt2fn("-xpm",NFILE,fnm);
else
epsfile=ftp2fn(efEPS,NFILE,fnm);
-
+ }
if (ecombine!=ecHalves && epsfile) {
fprintf(stderr,
"WARNING: can only write result of arithmetic combination "
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff