Updated manual and html pages, and changed version to 3.1.

Fixed a bug where gmx_sum was called without mpi.

diff --git a/admin/mkcompl b/admin/mkcompl
index 6a8f277a7e66e8ea8f85e82717c61c91da272c6c..d08f32907f3cf5bb7e401c70a5645f59c3f2f27e 100755 (executable)
--- a/admin/mkcompl
+++ b/admin/mkcompl
@@ -1,6 +1,6 @@
 #!/bin/csh -f
 
-# NB: Put the finished completions in the gromacs-3.0/scripts directory.
+# NB: Put the finished completions in the gromacs-3.1/scripts directory.
 
 if ( $#argv < 1 ) then
   echo "Error: provide the binary directory as first argument."

diff --git a/admin/mkhtml b/admin/mkhtml
index f2bdd00dfe1cb6445d7cc00bed03dae157de0550..59a55159b0d659b7c1c2781fcf1fca5e9e47e180 100755 (executable)
--- a/admin/mkhtml
+++ b/admin/mkhtml
@@ -51,13 +51,13 @@ cat > $HTMLIDX << EOD
 <td ALIGN=LEFT VALIGN=TOP WIDTH=280>
 <br><br>
 <h2>
-GROMACS 3.0<br>
+GROMACS 3.1<br>
 Online Reference</h2>
 </td>
 </TABLE></TD>
 <td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
-<B>VERSION 3.0<br>
-Tue 15 May 2001</B></td>
+<B>VERSION 3.1<br>
+Wed 27 Feb 2002</B></td>
 </tr>
 </table>
 
@@ -126,7 +126,6 @@ cat >> $HTMLIDX <<EOD
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </body>
 </html>
 EOD

diff --git a/configure.ac b/configure.ac
index 2a7400d192f4634920a73f9ddc2e160fd40e8073..7244b82f4fcb7083af169fd203df59d641504b20 100644 (file)
--- a/configure.ac
+++ b/configure.ac
@@ -3,12 +3,12 @@
 #######################################################################
 
 AC_PREREQ(2.50)
-AC_INIT(GROMACS, 3.1.beta_20020215, gmx-users@gromacs.org)
+AC_INIT(GROMACS, 3.1, gmx-users@gromacs.org)
 AC_CONFIG_SRCDIR(src/gmxlib/3dview.c)
 AC_CONFIG_AUX_DIR(config)
 AC_CANONICAL_HOST
 
-AM_INIT_AUTOMAKE(gromacs, 3.1.beta_20020215)
+AM_INIT_AUTOMAKE(gromacs, 3.1)
 AC_PREFIX_DEFAULT(/usr/local/gromacs)
 AM_CONFIG_HEADER(src/config.h)
 dnl This is the version info according to the libtool versioning system.

diff --git a/man/man1/do_dssp.1 b/man/man1/do_dssp.1
index 961420a7270726c5f478b9632ce9609b9d884627..141889a51206a5d36060f3e43e5f2d763263ef5a 100644 (file)
--- a/man/man1/do_dssp.1
+++ b/man/man1/do_dssp.1
@@ -1,7 +1,7 @@
-.TH do_dssp 1 "Mon 23 Jul 2001"
+.TH do_dssp 1 "Wed 27 Feb 2002"
 .SH NAME
 do_dssp
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3do_dssp\fP
 .BI "-f" " traj.xtc "
@@ -28,16 +28,16 @@ do_dssp
 reads a trajectory file and computes the secondary structure for
 each time frame 
 calling the dssp program. If you do not have the dssp program,
-get it. do_dssp assumes that the dssp executable is in
-/home/mdgroup/dssp/dssp. If that is not the case, then you should
+get it. do_dssp assumes that the dssp executable is
+/usr/local/bin/dssp. If this is not the case, then you should
 set an environment variable 
 .B DSSP
 pointing to the dssp
-executable as in: 
+executable, e.g.: 
 
 
 
-.B setenv DSSP /usr/local/bin/dssp
+.B setenv DSSP /opt/dssp/bin/dssp
 
 
 
@@ -63,7 +63,9 @@ Solvent accessible surface (SAS) per residue can be calculated, both in
 absolute values (A2) and in fractions of the maximal accessible
 surface of a residue. The maximal accessible surface is defined as
 the accessible surface of a residue in a chain of glycines.
-[B]Note[b] that the program 
+
+.B Note
+that the program 
 .B g_sas
 can also compute SAS
 and that is more efficient.

diff --git a/man/man1/editconf.1 b/man/man1/editconf.1
index 83262bcfe0ea1bc5457dad4b64563af57e508bc2..1268979c10843002a621cf48d3836894f9b5bc68 100644 (file)
--- a/man/man1/editconf.1
+++ b/man/man1/editconf.1
@@ -1,7 +1,7 @@
-.TH editconf 1 "Mon 23 Jul 2001"
+.TH editconf 1 "Wed 27 Feb 2002"
 .SH NAME
 editconf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3editconf\fP
 .BI "-f" " conf.gro "
@@ -203,7 +203,7 @@ 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
+.B editconf -f in -rotate 0 -45 -35.264 -bt o -box veclen -o out
 
 
 where 

diff --git a/man/man1/eneconv.1 b/man/man1/eneconv.1
index 76558906ba866d6508ca3ca71414f3a102db3da5..c5baec53e9ee1517faa7844ae066a17294156f29 100644 (file)
--- a/man/man1/eneconv.1
+++ b/man/man1/eneconv.1
@@ -1,7 +1,7 @@
-.TH eneconv 1 "Mon 23 Jul 2001"
+.TH eneconv 1 "Wed 27 Feb 2002"
 .SH NAME
 eneconv
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3eneconv\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_anaeig.1 b/man/man1/g_anaeig.1
index f5bc7079c1f62aabd06265d7462bb9452cbc9d87..e846b0fccdfb43aef074af8a3ccb978c85fac74e 100644 (file)
--- a/man/man1/g_anaeig.1
+++ b/man/man1/g_anaeig.1
@@ -1,7 +1,7 @@
-.TH g_anaeig 1 "Mon 23 Jul 2001"
+.TH g_anaeig 1 "Wed 27 Feb 2002"
 .SH NAME
 g_anaeig
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_anaeig\fP
 .BI "-v" " eigenvec.trr "

diff --git a/man/man1/g_analyze.1 b/man/man1/g_analyze.1
index b443733035f433a0d7474516913204774b5a0f48..57009351103f2dcd4b12cee8737cc4497ce07ffa 100644 (file)
--- a/man/man1/g_analyze.1
+++ b/man/man1/g_analyze.1
@@ -1,7 +1,7 @@
-.TH g_analyze 1 "Mon 23 Jul 2001"
+.TH g_analyze 1 "Wed 27 Feb 2002"
 .SH NAME
 g_analyze
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_analyze\fP
 .BI "-f" " graph.xvg "
@@ -11,6 +11,7 @@ g_analyze
 .BI "-dist" " distr.xvg "
 .BI "-av" " average.xvg "
 .BI "-ee" " errest.xvg "
+.BI "-g" " fitlog.log "
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
@@ -158,6 +159,10 @@ zero or negative value are ignored.
 .B Output, Opt.
  xvgr/xmgr file 
 
+.BI "-g" " fitlog.log" 
+.B Output, Opt.
+ Log file 
+
 .SH OTHER OPTIONS
 .BI "-[no]h"  "    no"
  Print help info and quit
@@ -235,8 +240,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_angle.1 b/man/man1/g_angle.1
index 4adc43de34cf1d9a04f75e8fe4cc4c21e8c45491..06358e551a23e0991ea49ca7448a45b57a8e10af 100644 (file)
--- a/man/man1/g_angle.1
+++ b/man/man1/g_angle.1
@@ -1,7 +1,7 @@
-.TH g_angle 1 "Mon 23 Jul 2001"
+.TH g_angle 1 "Wed 27 Feb 2002"
 .SH NAME
 g_angle
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_angle\fP
 .BI "-f" " traj.xtc "
@@ -159,8 +159,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_bond.1 b/man/man1/g_bond.1
index 442c2da3376950ee9de79a856b47478127366fcb..3840cf8563dfc87776b701f42d5a43333c90e703 100644 (file)
--- a/man/man1/g_bond.1
+++ b/man/man1/g_bond.1
@@ -1,13 +1,15 @@
-.TH g_bond 1 "Mon 23 Jul 2001"
+.TH g_bond 1 "Wed 27 Feb 2002"
 .SH NAME
 g_bond
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_bond\fP
 .BI "-f" " traj.xtc "
 .BI "-n" " index.ndx "
+.BI "-s" " topol.tpr "
 .BI "-o" " bonds.xvg "
 .BI "-l" " bonds.log "
+.BI "-d" " distance.xvg "
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
@@ -31,7 +33,14 @@ gives the half-width of the distribution as a fraction
 of the bondlength (
 .B -blen
 ). That means, for a bond of 0.2
-a tol of 0.1 gives a distribution from 0.18 to 0.22
+a tol of 0.1 gives a distribution from 0.18 to 0.22.
+
+
+Option 
+.B -d
+plots all the distances as a function of time.
+This requires a structure file for the atom and residue names in
+the output.
 .SH FILES
 .BI "-f" " traj.xtc" 
 .B Input
@@ -41,6 +50,10 @@ a tol of 0.1 gives a distribution from 0.18 to 0.22
 .B Input
  Index file 
 
+.BI "-s" " topol.tpr" 
+.B Input, Opt.
+ Structure+mass(db): tpr tpb tpa gro g96 pdb 
+
 .BI "-o" " bonds.xvg" 
 .B Output
  xvgr/xmgr file 
@@ -49,6 +62,10 @@ a tol of 0.1 gives a distribution from 0.18 to 0.22
 .B Output, Opt.
  Log file 
 
+.BI "-d" " distance.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
 .SH OTHER OPTIONS
 .BI "-[no]h"  "    no"
  Print help info and quit

diff --git a/man/man1/g_bundle.1 b/man/man1/g_bundle.1
index aaff86aa33576f97d568c0f27fbb53decbee1bd3..de792f2b16c0f75c578cf9e601fbfdb3ca63a1d8 100644 (file)
--- a/man/man1/g_bundle.1
+++ b/man/man1/g_bundle.1
@@ -1,7 +1,7 @@
-.TH g_bundle 1 "Mon 23 Jul 2001"
+.TH g_bundle 1 "Wed 27 Feb 2002"
 .SH NAME
 g_bundle
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_bundle\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_chi.1 b/man/man1/g_chi.1
index e6dd7ee516ad15ec77a8efd01cc44a985a33e6cb..503a7278fc1d7310d2689b4046617a9a322631c8 100644 (file)
--- a/man/man1/g_chi.1
+++ b/man/man1/g_chi.1
@@ -1,7 +1,7 @@
-.TH g_chi 1 "Mon 23 Jul 2001"
+.TH g_chi 1 "Wed 27 Feb 2002"
 .SH NAME
 g_chi
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_chi\fP
 .BI "-c" " conf.gro "
@@ -207,8 +207,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_cluster.1 b/man/man1/g_cluster.1
index d4dc0d7e48b455503d91ff7c8131c18815d6bd9c..7c83d377b17718c4b9dc5c5d37e7e742bb80344e 100644 (file)
--- a/man/man1/g_cluster.1
+++ b/man/man1/g_cluster.1
@@ -1,7 +1,7 @@
-.TH g_cluster 1 "Mon 23 Jul 2001"
+.TH g_cluster 1 "Wed 27 Feb 2002"
 .SH NAME
 g_cluster
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_cluster\fP
 .BI "-f" " traj.xtc "
@@ -29,6 +29,7 @@ g_cluster
 .BI "-nlevels" " int "
 .BI "-keepfree" " int "
 .BI "-cutoff" " real "
+.BI "-[no]fit" ""
 .BI "-max" " real "
 .BI "-skip" " int "
 .BI "-[no]av" ""
@@ -266,6 +267,9 @@ or
 .BI "-cutoff"  " real" "    0.1" 
  RMSD cut-off (nm) for two structures to be neighbor
 
+.BI "-[no]fit"  "   yes"
+ Use least squares fitting before RMSD calculation
+
 .BI "-max"  " real" "     -1" 
  Maximum level in RMSD matrix
 

diff --git a/man/man1/g_confrms.1 b/man/man1/g_confrms.1
index 44c71fd103d61b7092f99e76facca432d6fcdea4..f3b521f82a2e72561f8ff76561596c665a9d01f5 100644 (file)
--- a/man/man1/g_confrms.1
+++ b/man/man1/g_confrms.1
@@ -1,7 +1,7 @@
-.TH g_confrms 1 "Mon 23 Jul 2001"
+.TH g_confrms 1 "Wed 27 Feb 2002"
 .SH NAME
 g_confrms
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_confrms\fP
 .BI "-f1" " conf1.gro "

diff --git a/man/man1/g_covar.1 b/man/man1/g_covar.1
index 01a84306fcf6525574a6f0df2f8d39747049390a..b7b4d5d0cd8b0d732e46743df6855afbe56edf30 100644 (file)
--- a/man/man1/g_covar.1
+++ b/man/man1/g_covar.1
@@ -1,7 +1,7 @@
-.TH g_covar 1 "Mon 23 Jul 2001"
+.TH g_covar 1 "Wed 27 Feb 2002"
 .SH NAME
 g_covar
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_covar\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_density.1 b/man/man1/g_density.1
index 305f38a7fdc2507f585103cb6017ee056eecaf2e..e63e618bc53a72183553e532f9b6385fffa1f57c 100644 (file)
--- a/man/man1/g_density.1
+++ b/man/man1/g_density.1
@@ -1,7 +1,7 @@
-.TH g_density 1 "Mon 23 Jul 2001"
+.TH g_density 1 "Wed 27 Feb 2002"
 .SH NAME
 g_density
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_density\fP
 .BI "-f" " traj.xtc "
@@ -23,8 +23,22 @@ g_density
 .BI "-[no]count" ""
 .SH DESCRIPTION
 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
+in kg/m3, number densities or electron densities can be
+calculated. For electron densities, a file describing the number of
+electrons for each type of atom should be provided using 
+.B -ei
+.
+It should look like:
+
+   2
+
+   atomname = nrelectrons
+
+   atomname = nrelectrons
+
+The first line contains the number of lines to read from the file.
+There should be one line for each unique atom name in your system.
+The number of electrons for each atom is modified by its atomic
 partial charge.
 .SH FILES
 .BI "-f" " traj.xtc" 
@@ -40,7 +54,7 @@ partial charge.
  Generic run input: tpr tpb tpa 
 
 .BI "-ei" " electrons.dat" 
-.B Output
+.B Input, Opt.
  Generic data file 
 
 .BI "-o" " density.xvg" 

diff --git a/man/man1/g_dielectric.1 b/man/man1/g_dielectric.1
index 61732e338d10bff3646371f29328075642cbf057..9940d2cf5228f907ec0bc89703d638c90ff6bbbb 100644 (file)
--- a/man/man1/g_dielectric.1
+++ b/man/man1/g_dielectric.1
@@ -1,7 +1,7 @@
-.TH g_dielectric 1 "Mon 23 Jul 2001"
+.TH g_dielectric 1 "Wed 27 Feb 2002"
 .SH NAME
 g_dielectric
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_dielectric\fP
 .BI "-f" " Mtot.xvg "
@@ -140,8 +140,12 @@ plot should be one half of a circle
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-nsmooth"  " int" " 3" 

diff --git a/man/man1/g_dih.1 b/man/man1/g_dih.1
index d01ccc5befc6bfaf20a0790aadc6ab8387754528..073b2e459382a2377b562ecd8ad778ff78fdc5cb 100644 (file)
--- a/man/man1/g_dih.1
+++ b/man/man1/g_dih.1
@@ -1,7 +1,7 @@
-.TH g_dih 1 "Mon 23 Jul 2001"
+.TH g_dih 1 "Wed 27 Feb 2002"
 .SH NAME
 g_dih
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_dih\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_dipoles.1 b/man/man1/g_dipoles.1
index 9b8b831b3b5f27c2870dbc6fd6aa7f82a6baac8e..df3dc031ee9533d60be587fb4494ba62eb5e4e8b 100644 (file)
--- a/man/man1/g_dipoles.1
+++ b/man/man1/g_dipoles.1
@@ -1,7 +1,7 @@
-.TH g_dipoles 1 "Mon 23 Jul 2001"
+.TH g_dipoles 1 "Wed 27 Feb 2002"
 .SH NAME
 g_dipoles
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_dipoles\fP
 .BI "-enx" " ener.edr "
@@ -66,7 +66,9 @@ Option
 produces a plot of the distance dependent Kirkwood
 G-factor, as well as the average cosine of the angle between the dipoles
 as a function of the distance. The plot also includes gOO and hOO
-according to Nymand & Linse, JCP 112 (2000) pp 6386-6395.
+according to Nymand & Linse, JCP 112 (2000) pp 6386-6395. In the same plot
+we also include the energy per scale computed by taking the inner product of
+the dipoles divided by the distance to the third power.
 
 
 
@@ -200,8 +202,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_disre.1 b/man/man1/g_disre.1
index 52e643ebfcd081aca575c737f27912c10223ebf7..e993e16140d774635cdb0be65cb8d623864cc2f2 100644 (file)
--- a/man/man1/g_disre.1
+++ b/man/man1/g_disre.1
@@ -1,7 +1,7 @@
-.TH g_disre 1 "Mon 23 Jul 2001"
+.TH g_disre 1 "Wed 27 Feb 2002"
 .SH NAME
 g_disre
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_disre\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_dist.1 b/man/man1/g_dist.1
index d3b24e1335d4a436dd0bc900883aafbcae75dc0c..ebf3bc63a441481147d3c09db035d952562793f6 100644 (file)
--- a/man/man1/g_dist.1
+++ b/man/man1/g_dist.1
@@ -1,7 +1,7 @@
-.TH g_dist 1 "Mon 23 Jul 2001"
+.TH g_dist 1 "Wed 27 Feb 2002"
 .SH NAME
 g_dist
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_dist\fP
 .BI "-f" " traj.xtc "
@@ -25,6 +25,14 @@ Or when
 .B -dist
 is set, print all the atoms in group 2 that are
 closer than a certain distance to the center of mass of group 1.
+
+
+Other programs that calculate distances are 
+.B g_mindist
+
+and 
+.B g_bond
+.
 .SH FILES
 .BI "-f" " traj.xtc" 
 .B Input

diff --git a/man/man1/g_dyndom.1 b/man/man1/g_dyndom.1
index 9b04d985435b141a5d806e3c8950cd05fd8279b1..aa7a6c83724834e3488f54dd6e977cdc1c054c58 100644 (file)
--- a/man/man1/g_dyndom.1
+++ b/man/man1/g_dyndom.1
@@ -1,7 +1,7 @@
-.TH g_dyndom 1 "Mon 23 Jul 2001"
+.TH g_dyndom 1 "Wed 27 Feb 2002"
 .SH NAME
 g_dyndom
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_dyndom\fP
 .BI "-f" " dyndom.pdb "

diff --git a/man/man1/g_enemat.1 b/man/man1/g_enemat.1
index c519741ada54601508db9d2135548a7aeabf6b68..e1c50468e36da2ba4306467df1c438143256bd2d 100644 (file)
--- a/man/man1/g_enemat.1
+++ b/man/man1/g_enemat.1
@@ -1,7 +1,7 @@
-.TH g_enemat 1 "Mon 23 Jul 2001"
+.TH g_enemat 1 "Wed 27 Feb 2002"
 .SH NAME
 g_enemat
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_enemat\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_energy.1 b/man/man1/g_energy.1
index 3f719171acd7d4376e545d97108ae57cf4ea6ebb..1a75340e133e5d0d720e7a246a487d343083b5d0 100644 (file)
--- a/man/man1/g_energy.1
+++ b/man/man1/g_energy.1
@@ -1,7 +1,7 @@
-.TH g_energy 1 "Mon 23 Jul 2001"
+.TH g_energy 1 "Wed 27 Feb 2002"
 .SH NAME
 g_energy
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_energy\fP
 .BI "-f" " ener.edr "
@@ -10,6 +10,11 @@ g_energy
 .BI "-o" " energy.xvg "
 .BI "-viol" " violaver.xvg "
 .BI "-pairs" " pairs.xvg "
+.BI "-ora" " orienta.xvg "
+.BI "-ort" " orientt.xvg "
+.BI "-oda" " orideva.xvg "
+.BI "-odr" " oridevr.xvg "
+.BI "-odt" " oridevt.xvg "
 .BI "-corr" " enecorr.xvg "
 .BI "-vis" " visco.xvg "
 .BI "-ravg" " runavgdf.xvg "
@@ -30,6 +35,7 @@ g_energy
 .BI "-nmol" " int "
 .BI "-ndf" " int "
 .BI "-[no]fluc" ""
+.BI "-[no]orinst" ""
 .BI "-acflen" " int "
 .BI "-[no]normalize" ""
 .BI "-P" " enum "
@@ -43,6 +49,12 @@ data from an energy file. The user is prompted to interactively
 select the energy terms she wants.
 
 
+Average and RMSD are calculated with full precision from the
+simulation (see printed manual). Drift is calculated by performing
+a LSQ fit of the data to a straight line. Total drift is drift
+multiplied by total time.
+
+
 When the 
 .B -viol
 option is set, the time averaged
@@ -54,10 +66,33 @@ selected pairs can be plotted with the
 option.
 
 
-Average and RMSD are calculated with full precision from the
-simulation (see printed manual). Drift is calculated by performing
-a LSQ fit of the data to a straight line. Total drift is drift
-multiplied by total time.
+Options 
+.B -ora
+, 
+.B -ort
+, 
+.B -oda
+, 
+.B -odr
+and
+
+.B -odt
+are used for analyzing orientation restraint data.
+The first two options plot the orientation, the last three the
+deviations of the orientations from the experimental values.
+The options that end on an 'a' plot the average over time
+as a function of restraint. The options that end on a 't'
+prompt the user for restraint label numbers and plot the data
+as a function of time. Option 
+.B -odr
+plots the RMS
+deviation as a function of restraint.
+When the run used time or ensemble averaged orientation restraints,
+option 
+.B -orinst
+can be used to analyse the instantaneous,
+not ensemble-averaged orientations and deviations instead of
+the time and ensemble averages.
 
 
 With 
@@ -108,6 +143,26 @@ the energies must both be calculated from the same trajectory.
 .B Output, Opt.
  xvgr/xmgr file 
 
+.BI "-ora" " orienta.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-ort" " orientt.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-oda" " orideva.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-odr" " oridevr.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-odt" " oridevt.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
 .BI "-corr" " enecorr.xvg" 
 .B Output, Opt.
  xvgr/xmgr file 
@@ -172,6 +227,9 @@ the energies must both be calculated from the same trajectory.
 .BI "-[no]fluc"  "    no"
  Calculate autocorrelation of energy fluctuations rather than energy itself
 
+.BI "-[no]orinst"  "    no"
+ Analyse instantaneous orientation data
+
 .BI "-acflen"  " int" " -1" 
  Length of the ACF, default is half the number of frames
 
@@ -198,8 +256,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_gyrate.1 b/man/man1/g_gyrate.1
index ede96bacd13b2600ac0155138919091fd25934ab..6326e34207a288b974d4ea7af4353eef018f2e44 100644 (file)
--- a/man/man1/g_gyrate.1
+++ b/man/man1/g_gyrate.1
@@ -1,7 +1,7 @@
-.TH g_gyrate 1 "Mon 23 Jul 2001"
+.TH g_gyrate 1 "Wed 27 Feb 2002"
 .SH NAME
 g_gyrate
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_gyrate\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_h2order.1 b/man/man1/g_h2order.1
index 4e6aba4801779ecc6276e59aa6e5f8c801adc1d3..62a1ecfce8e06085dafc6b7bb525dc008d2b3b07 100644 (file)
--- a/man/man1/g_h2order.1
+++ b/man/man1/g_h2order.1
@@ -1,7 +1,7 @@
-.TH g_h2order 1 "Mon 23 Jul 2001"
+.TH g_h2order 1 "Wed 27 Feb 2002"
 .SH NAME
 g_h2order
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_h2order\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_hbond.1 b/man/man1/g_hbond.1
index 09ae48ed239a25840e9b05a9a03be26ca958ac58..c908a10982ce30ae742d73bea7eb857dc0f4c645 100644 (file)
--- a/man/man1/g_hbond.1
+++ b/man/man1/g_hbond.1
@@ -1,7 +1,7 @@
-.TH g_hbond 1 "Mon 23 Jul 2001"
+.TH g_hbond 1 "Wed 27 Feb 2002"
 .SH NAME
 g_hbond
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_hbond\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_helix.1 b/man/man1/g_helix.1
index 5a57df0d0ba0858faa1d4b7255ae97acc096982e..3b9ccb8a701964d7734008407188e53009329481 100644 (file)
--- a/man/man1/g_helix.1
+++ b/man/man1/g_helix.1
@@ -1,7 +1,7 @@
-.TH g_helix 1 "Mon 23 Jul 2001"
+.TH g_helix 1 "Wed 27 Feb 2002"
 .SH NAME
 g_helix
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_helix\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_lie.1 b/man/man1/g_lie.1
index f42cb258cccba287167ae91da4eafb328b732374..bda330c1c06cf798a570b62f9446d8abac3eb4b6 100644 (file)
--- a/man/man1/g_lie.1
+++ b/man/man1/g_lie.1
@@ -1,7 +1,7 @@
-.TH g_lie 1 "Mon 23 Jul 2001"
+.TH g_lie 1 "Wed 27 Feb 2002"
 .SH NAME
 g_lie
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_lie\fP
 .BI "-f" " ener.edr "

diff --git a/man/man1/g_mdmat.1 b/man/man1/g_mdmat.1
index 11a4b0bbdc47750e8e761456de927133d3777a49..947d2c43c842adfaae991beb1525141cfe421a9d 100644 (file)
--- a/man/man1/g_mdmat.1
+++ b/man/man1/g_mdmat.1
@@ -1,7 +1,7 @@
-.TH g_mdmat 1 "Mon 23 Jul 2001"
+.TH g_mdmat 1 "Wed 27 Feb 2002"
 .SH NAME
 g_mdmat
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_mdmat\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_mindist.1 b/man/man1/g_mindist.1
index 9338a2735e55b12d8d4ae0d88372d5614bfe0dc0..ae76dfad517cd60337191a3971f9ecfec5900233 100644 (file)
--- a/man/man1/g_mindist.1
+++ b/man/man1/g_mindist.1
@@ -1,7 +1,7 @@
-.TH g_mindist 1 "Mon 23 Jul 2001"
+.TH g_mindist 1 "Wed 27 Feb 2002"
 .SH NAME
 g_mindist
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_mindist\fP
 .BI "-f" " traj.xtc "
@@ -34,8 +34,15 @@ periodic image is plotted. This is useful for checking if a protein
 has seen its periodic image during a simulation. Only one shift in
 each direction is considered, giving a total of 26 shifts.
 It also plots the maximum distance within the group and the lengths
-of the three box vectors.
-This option is very slow.
+of the three box vectors. This option is very slow.
+
+
+Other programs that calculate distances are 
+.B g_dist
+
+and 
+.B g_bond
+.
 .SH FILES
 .BI "-f" " traj.xtc" 
 .B Input

diff --git a/man/man1/g_morph.1 b/man/man1/g_morph.1
index c223e92835fd9dd44bb29da16a55b2b27cbe4a16..18a51df00f5c3e5b448eb1cb2e7a357b5c97547b 100644 (file)
--- a/man/man1/g_morph.1
+++ b/man/man1/g_morph.1
@@ -1,7 +1,7 @@
-.TH g_morph 1 "Mon 23 Jul 2001"
+.TH g_morph 1 "Wed 27 Feb 2002"
 .SH NAME
 g_morph
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_morph\fP
 .BI "-f1" " conf1.gro "

diff --git a/man/man1/g_msd.1 b/man/man1/g_msd.1
index 890192f8775b7c6323c91ca0ca9050f5ff44655f..0589bce1f7c292c2a4a98ec762e14c7cc0932c29 100644 (file)
--- a/man/man1/g_msd.1
+++ b/man/man1/g_msd.1
@@ -1,7 +1,7 @@
-.TH g_msd 1 "Mon 23 Jul 2001"
+.TH g_msd 1 "Wed 27 Feb 2002"
 .SH NAME
 g_msd
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_msd\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_nmeig.1 b/man/man1/g_nmeig.1
index 82d9c1413d33409dcff94bdd1c327335416bf3b5..5ea15bb047edbf1379e6c65752c2c113cae0cdd4 100644 (file)
--- a/man/man1/g_nmeig.1
+++ b/man/man1/g_nmeig.1
@@ -1,7 +1,7 @@
-.TH g_nmeig 1 "Mon 23 Jul 2001"
+.TH g_nmeig 1 "Wed 27 Feb 2002"
 .SH NAME
 g_nmeig
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_nmeig\fP
 .BI "-f" " hessian.mtx "

diff --git a/man/man1/g_nmens.1 b/man/man1/g_nmens.1
index c65b82ce5d6b2490cac6297f56714f1d0e24db05..1811df1b91fb82c422eefcc0f6b52f65ecd18448 100644 (file)
--- a/man/man1/g_nmens.1
+++ b/man/man1/g_nmens.1
@@ -1,7 +1,7 @@
-.TH g_nmens 1 "Mon 23 Jul 2001"
+.TH g_nmens 1 "Wed 27 Feb 2002"
 .SH NAME
 g_nmens
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_nmens\fP
 .BI "-v" " eigenvec.trr "

diff --git a/man/man1/g_order.1 b/man/man1/g_order.1
index 33b1a90cc33df270ea50985c60c4c0a0f5dd9183..1b44e00a2a5dba6c4520da7d06668f1c9f6d301e 100644 (file)
--- a/man/man1/g_order.1
+++ b/man/man1/g_order.1
@@ -1,7 +1,7 @@
-.TH g_order 1 "Mon 23 Jul 2001"
+.TH g_order 1 "Wed 27 Feb 2002"
 .SH NAME
 g_order
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_order\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_potential.1 b/man/man1/g_potential.1
index 7ef24cdfb8606fe213a2fdda518208f401278422..40c9a52542aebac3af71d6fd43e4ed79a6181a16 100644 (file)
--- a/man/man1/g_potential.1
+++ b/man/man1/g_potential.1
@@ -1,7 +1,7 @@
-.TH g_potential 1 "Mon 23 Jul 2001"
+.TH g_potential 1 "Wed 27 Feb 2002"
 .SH NAME
 g_potential
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_potential\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rama.1 b/man/man1/g_rama.1
index bfc7e580078ab56e0739861394f2754d9c72ace8..fc5888cbae5f45322f1f7b0e34f0dfaf07a02644 100644 (file)
--- a/man/man1/g_rama.1
+++ b/man/man1/g_rama.1
@@ -1,7 +1,7 @@
-.TH g_rama 1 "Mon 23 Jul 2001"
+.TH g_rama 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rama
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rama\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rdf.1 b/man/man1/g_rdf.1
index ea71d3058e2a35380962dfa18fc24bc029a14bc8..af901cef0489c29f0bec03de5edc72d1ada9c3f9 100644 (file)
--- a/man/man1/g_rdf.1
+++ b/man/man1/g_rdf.1
@@ -1,7 +1,7 @@
-.TH g_rdf 1 "Mon 23 Jul 2001"
+.TH g_rdf 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rdf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rdf\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rms.1 b/man/man1/g_rms.1
index aede270a382469ca09468fa61f2410df130fc5a5..6de7ebac815e686d74bfe2f0cd426cc80c07cbd8 100644 (file)
--- a/man/man1/g_rms.1
+++ b/man/man1/g_rms.1
@@ -1,7 +1,7 @@
-.TH g_rms 1 "Mon 23 Jul 2001"
+.TH g_rms 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rms
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rms\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/g_rmsdist.1 b/man/man1/g_rmsdist.1
index eab6167824a6d5ba1a10d93574cbfe8c4fe8158d..e61950204d2f5d18d63cb49de21405d513b3fc92 100644 (file)
--- a/man/man1/g_rmsdist.1
+++ b/man/man1/g_rmsdist.1
@@ -1,7 +1,7 @@
-.TH g_rmsdist 1 "Mon 23 Jul 2001"
+.TH g_rmsdist 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rmsdist
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rmsdist\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rmsf.1 b/man/man1/g_rmsf.1
index 3001155e390de2a67e5a1e5b7256746ae371619e..52276910b7b5c5634fab9802387ffe715d4e3122 100644 (file)
--- a/man/man1/g_rmsf.1
+++ b/man/man1/g_rmsf.1
@@ -1,7 +1,7 @@
-.TH g_rmsf 1 "Mon 23 Jul 2001"
+.TH g_rmsf 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rmsf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rmsf\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_rotacf.1 b/man/man1/g_rotacf.1
index ef95625e65eee4bbce8e41861a2a06271beeadd2..50cfdfedcd8fb96a5a15f71b0d5a30d4748246d2 100644 (file)
--- a/man/man1/g_rotacf.1
+++ b/man/man1/g_rotacf.1
@@ -1,7 +1,7 @@
-.TH g_rotacf 1 "Mon 23 Jul 2001"
+.TH g_rotacf 1 "Wed 27 Feb 2002"
 .SH NAME
 g_rotacf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_rotacf\fP
 .BI "-f" " traj.xtc "
@@ -120,8 +120,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/g_saltbr.1 b/man/man1/g_saltbr.1
index 1fe07faa9d18916097a7bfa361677d71f5f6d755..5e3898128e96bad18a0d7d0f22f800865846b6cb 100644 (file)
--- a/man/man1/g_saltbr.1
+++ b/man/man1/g_saltbr.1
@@ -1,7 +1,7 @@
-.TH g_saltbr 1 "Mon 23 Jul 2001"
+.TH g_saltbr 1 "Wed 27 Feb 2002"
 .SH NAME
 g_saltbr
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_saltbr\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_sas.1 b/man/man1/g_sas.1
index ee0de968c8225d3cf02bb871ddd2af3159b270fb..bbd7612ca5feb4ec5530ce2dd3bf9c0b6dd66f59 100644 (file)
--- a/man/man1/g_sas.1
+++ b/man/man1/g_sas.1
@@ -1,7 +1,7 @@
-.TH g_sas 1 "Mon 23 Jul 2001"
+.TH g_sas 1 "Wed 27 Feb 2002"
 .SH NAME
 g_sas
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_sas\fP
 .BI "-f" " traj.xtc "
@@ -24,9 +24,11 @@ g_sas
 .BI "-qmax" " real "
 .BI "-minarea" " real "
 .BI "-skip" " int "
+.BI "-[no]pbc" ""
 .BI "-[no]prot" ""
+.BI "-dgs" " real "
 .SH DESCRIPTION
-g_sas computes hydrophobic and total solvent accessible surface area.
+g_sas computes hydrophobic, hydrophilic and total solvent accessible surface area.
 As a side effect the Connolly surface can be generated as well in
 a pdb file where the nodes are represented as atoms and the vertices
 connecting the nearest nodes as CONECT records. The area can be plotted
@@ -35,6 +37,10 @@ the latter option an
 .B itp
 file can be generated (option -i)
 which can be used to restrain surface atoms.
+
+
+By default, periodic boundary conditions are taken into account,
+this can be turned off using the -pbc option.
 .SH FILES
 .BI "-f" " traj.xtc" 
 .B Input
@@ -100,11 +106,17 @@ which can be used to restrain surface atoms.
  The maximum charge (e, absolute value) of a hydrophobic atom
 
 .BI "-minarea"  " real" "    0.5" 
- The maximum charge (e, absolute value) of a hydrophobic atom
+ The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file  (see help)
 
 .BI "-skip"  " int" " 1" 
  Do only every nth frame
 
+.BI "-[no]pbc"  "   yes"
+ Take periodicity into account
+
 .BI "-[no]prot"  "   yes"
  Output the protein to the connelly pdb file too
 
+.BI "-dgs"  " real" "      0" 
+ default value for solvation free energy per area (kJ/mol/nm2)
+

diff --git a/man/man1/g_sgangle.1 b/man/man1/g_sgangle.1
index a410f16f7e459fb9c52fc5c010fd90b9a0c877cf..42a84f9b8467ed4bfd1b60a72d1464b2e66d894a 100644 (file)
--- a/man/man1/g_sgangle.1
+++ b/man/man1/g_sgangle.1
@@ -1,7 +1,7 @@
-.TH g_sgangle 1 "Mon 23 Jul 2001"
+.TH g_sgangle 1 "Wed 27 Feb 2002"
 .SH NAME
 g_sgangle
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_sgangle\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_sorient.1 b/man/man1/g_sorient.1
index b000332fa38d1bbb01868f9633afb46563ea5a1d..1f8741c8f4e11ae2f9cc8435f0f27f80553bc921 100644 (file)
--- a/man/man1/g_sorient.1
+++ b/man/man1/g_sorient.1
@@ -1,7 +1,7 @@
-.TH g_sorient 1 "Mon 23 Jul 2001"
+.TH g_sorient 1 "Wed 27 Feb 2002"
 .SH NAME
 g_sorient
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_sorient\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/g_tcaf.1 b/man/man1/g_tcaf.1
index 600d627cbd8b893bd8f61aaacd40522f00e919d6..4deed033db673c0ccfcda0ec0df433341d244d99 100644 (file)
--- a/man/man1/g_tcaf.1
+++ b/man/man1/g_tcaf.1
@@ -1,7 +1,7 @@
-.TH g_tcaf 1 "Mon 23 Jul 2001"
+.TH g_tcaf 1 "Wed 27 Feb 2002"
 .SH NAME
 g_tcaf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_tcaf\fP
 .BI "-f" " traj.trr "

diff --git a/man/man1/g_traj.1 b/man/man1/g_traj.1
index 2edf88c16600465a7ae6c4921f4d51b97889c4d7..a16537651b9678fc0fed1da179d48f614ff42a40 100644 (file)
--- a/man/man1/g_traj.1
+++ b/man/man1/g_traj.1
@@ -1,7 +1,7 @@
-.TH g_traj 1 "Mon 23 Jul 2001"
+.TH g_traj 1 "Wed 27 Feb 2002"
 .SH NAME
 g_traj
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_traj\fP
 .BI "-f" " traj.xtc "
@@ -12,7 +12,10 @@ g_traj
 .BI "-of" " force.xvg "
 .BI "-ob" " box.xvg "
 .BI "-ot" " temp.xvg "
+.BI "-ekt" " ektrans.xvg "
 .BI "-ekr" " ekrot.xvg "
+.BI "-cv" " veloc.pdb "
+.BI "-cf" " force.pdb "
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
@@ -46,18 +49,42 @@ is used for each molecule.
 Option 
 .B -ot
 plots the temperature of each group,
-provided velocities are present in the trajectory file.This implies 
+provided velocities are present in the trajectory file.
+No corrections are made for constrained degrees of freedom!
+This implies 
 .B -com
 .
 
 
-Option 
+Options 
+.B -ekt
+and 
 .B -ekr
-plots the rotational kinetic energy of each group,
+plot the translational and
+rotational kinetic energy of each group,
 provided velocities are present in the trajectory file.
 This implies 
 .B -com
 .
+
+
+Options 
+.B -cv
+and 
+.B -cf
+write the average velocities
+and average forces as temperature factors to a pdb file with
+the average coordinates. The temperature factors are scaled such
+that the maximum is 10. To get the velocities or forces of one
+frame set both 
+.B -b
+and 
+.B -e
+to the time of
+desired frame. When averaging over frames you might need to use
+the 
+.B -nojump
+option to obtain the correct average coordinates.
 .SH FILES
 .BI "-f" " traj.xtc" 
 .B Input
@@ -91,10 +118,22 @@ This implies
 .B Output, Opt.
  xvgr/xmgr file 
 
+.BI "-ekt" " ektrans.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
 .BI "-ekr" " ekrot.xvg" 
 .B Output, Opt.
  xvgr/xmgr file 
 
+.BI "-cv" " veloc.pdb" 
+.B Output, Opt.
+ Protein data bank file 
+
+.BI "-cf" " force.pdb" 
+.B Output, Opt.
+ Protein data bank file 
+
 .SH OTHER OPTIONS
 .BI "-[no]h"  "    no"
  Print help info and quit

diff --git a/man/man1/g_velacc.1 b/man/man1/g_velacc.1
index 557a96c7692d42676a5e84372c37714a3bc420a6..38fde119e0b0765fea0f04e6cb2422e3e345c65f 100644 (file)
--- a/man/man1/g_velacc.1
+++ b/man/man1/g_velacc.1
@@ -1,7 +1,7 @@
-.TH g_velacc 1 "Mon 23 Jul 2001"
+.TH g_velacc 1 "Wed 27 Feb 2002"
 .SH NAME
 g_velacc
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3g_velacc\fP
 .BI "-f" " traj.trr "
@@ -104,8 +104,12 @@ or
 .B aexp
 , 
 .B exp_exp
-or 
+, 
 .B vac
+, 
+.B exp5
+or 
+.B exp7
 
 
 .BI "-ncskip"  " int" " 0" 

diff --git a/man/man1/genbox.1 b/man/man1/genbox.1
index bb547bf4fbb5f2f91d3bc24eb79d5f763d651506..c08a67bdcfdd944bdc65905fcc2addbdb5393c7d 100644 (file)
--- a/man/man1/genbox.1
+++ b/man/man1/genbox.1
@@ -1,7 +1,7 @@
-.TH genbox 1 "Mon 23 Jul 2001"
+.TH genbox 1 "Wed 27 Feb 2002"
 .SH NAME
 genbox
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3genbox\fP
 .BI "-cp" " protein.gro "
@@ -75,8 +75,8 @@ times before giving up.
 Increase -try if you have several small holes to fill.
 
 
-The default solvent is Simple Point Charge water (SPC). The coordinates 
-for this are read from 
+The default solvent is Simple Point Charge water (SPC), with coordinates 
+from 
 .B $GMXLIB/spc216.gro
 . Other
 solvents are also supported, as well as mixed solvents. The

diff --git a/man/man1/genconf.1 b/man/man1/genconf.1
index a7e3c368f80d216c5f326877dd2fe11732e118e8..b2c92fe10deb0ffd5f57c1ac8608ecf68d2f1163 100644 (file)
--- a/man/man1/genconf.1
+++ b/man/man1/genconf.1
@@ -1,7 +1,7 @@
-.TH genconf 1 "Mon 23 Jul 2001"
+.TH genconf 1 "Wed 27 Feb 2002"
 .SH NAME
 genconf
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3genconf\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/genion.1 b/man/man1/genion.1
index cb60ea4e00cfec64227336cd8fd7e2f0f3070793..ec7a537e62343378c400bdb99793540909df9add 100644 (file)
--- a/man/man1/genion.1
+++ b/man/man1/genion.1
@@ -1,7 +1,7 @@
-.TH genion 1 "Mon 23 Jul 2001"
+.TH genion 1 "Wed 27 Feb 2002"
 .SH NAME
 genion
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3genion\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/genpr.1 b/man/man1/genpr.1
index edf4106daea2430e2ddfaddd9e8f5cf8bdbcee63..1412f1af318f7d733ccbc38e33ed90f3bbf1724a 100644 (file)
--- a/man/man1/genpr.1
+++ b/man/man1/genpr.1
@@ -1,7 +1,7 @@
-.TH genpr 1 "Mon 23 Jul 2001"
+.TH genpr 1 "Wed 27 Feb 2002"
 .SH NAME
 genpr
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3genpr\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/gmxcheck.1 b/man/man1/gmxcheck.1
index f1b049780fde72327e1a277ce9ee513f87551c39..7218e0fe66bfe28913d8fc703339c73fbe966540 100644 (file)
--- a/man/man1/gmxcheck.1
+++ b/man/man1/gmxcheck.1
@@ -1,7 +1,7 @@
-.TH gmxcheck 1 "Mon 23 Jul 2001"
+.TH gmxcheck 1 "Wed 27 Feb 2002"
 .SH NAME
 gmxcheck
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3gmxcheck\fP
 .BI "-f" " traj.xtc "
@@ -18,6 +18,7 @@ gmxcheck
 .BI "-bonlo" " real "
 .BI "-bonhi" " real "
 .BI "-tol" " real "
+.BI "-lastener" " string "
 .SH DESCRIPTION
 gmxcheck reads a trajectory (
 .B .trj
@@ -113,5 +114,8 @@ are supplied.
  Max. fract. of sum of VdW radii for bonded atoms
 
 .BI "-tol"  " real" "      0" 
- Tolerance for comparing real values
+ Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|)
+
+.BI "-lastener"  " string" " " 
+ Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.
 

diff --git a/man/man1/gmxdump.1 b/man/man1/gmxdump.1
index 7f2e32aa25484ae8f424a9369a70eedcfd4a9d3f..d6fc34cf06662e8651cec9712dcd4ccafabf042f 100644 (file)
--- a/man/man1/gmxdump.1
+++ b/man/man1/gmxdump.1
@@ -1,7 +1,7 @@
-.TH gmxdump 1 "Mon 23 Jul 2001"
+.TH gmxdump 1 "Wed 27 Feb 2002"
 .SH NAME
 gmxdump
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3gmxdump\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/grompp.1 b/man/man1/grompp.1
index 10a3accd9302623e782e57d7207e790f0d2588f3..d46cc763eab6effbaf51fc642430d76eb909b8c1 100644 (file)
--- a/man/man1/grompp.1
+++ b/man/man1/grompp.1
@@ -1,7 +1,7 @@
-.TH grompp 1 "Mon 23 Jul 2001"
+.TH grompp 1 "Wed 27 Feb 2002"
 .SH NAME
 grompp
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3grompp\fP
 .BI "-f" " grompp.mdp "
@@ -46,6 +46,15 @@ Eventually a binary file is produced that can serve as the sole input
 file for the MD program.
 
 
+grompp uses the atom names from the topology file. The atom names
+in the coordinate file (option 
+.B -c
+) are only read to generate
+warnings when they do not match the atom names in the topology.
+Note that the atom names are irrelevant for the simulation as
+only the atom types are used for generating interaction parameters.
+
+
 grompp calls the c-preprocessor to resolve includes, macros 
 etcetera. To specify a macro-preprocessor other than /lib/cpp 
 (such as m4)
@@ -150,7 +159,7 @@ can see the contents of the run input file with the
 program.
 .SH FILES
 .BI "-f" " grompp.mdp" 
-.B Input
+.B Input, Opt.
  grompp input file with MD parameters 
 
 .BI "-po" " mdout.mdp" 

diff --git a/man/man1/highway.1 b/man/man1/highway.1
index 5207e63514e2237cf8ec4dace2d89b71eb976201..bd966b743153049e7d49277dd5a3fd5a20beae5a 100644 (file)
--- a/man/man1/highway.1
+++ b/man/man1/highway.1
@@ -1,7 +1,7 @@
-.TH highway 1 "Mon 23 Jul 2001"
+.TH highway 1 "Wed 27 Feb 2002"
 .SH NAME
 highway
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3highway\fP
 .BI "-f" " highway.dat "

diff --git a/man/man1/make_ndx.1 b/man/man1/make_ndx.1
index 8bf5119d9968e98e54b3e52e4cf69acfaa12d034..06828c38f86504333fa09a30480b1492c5b32903 100644 (file)
--- a/man/man1/make_ndx.1
+++ b/man/man1/make_ndx.1
@@ -1,7 +1,7 @@
-.TH make_ndx 1 "Mon 23 Jul 2001"
+.TH make_ndx 1 "Wed 27 Feb 2002"
 .SH NAME
 make_ndx
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3make_ndx\fP
 .BI "-f" " conf.gro "

diff --git a/man/man1/mdrun.1 b/man/man1/mdrun.1
index 034f51bc6e4a53b67f07e7420f701aa845357d88..14fd9888358c0fe51e3cfee1f5626d7c6d3f03ba 100644 (file)
--- a/man/man1/mdrun.1
+++ b/man/man1/mdrun.1
@@ -1,7 +1,7 @@
-.TH mdrun 1 "Mon 23 Jul 2001"
+.TH mdrun 1 "Wed 27 Feb 2002"
 .SH NAME
 mdrun
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3mdrun\fP
 .BI "-s" " topol.tpr "
@@ -15,10 +15,16 @@ mdrun
 .BI "-rerun" " rerun.xtc "
 .BI "-ei" " sam.edi "
 .BI "-eo" " sam.edo "
+.BI "-j" " wham.gct "
+.BI "-jo" " bam.gct "
+.BI "-ffout" " gct.xvg "
+.BI "-devout" " deviatie.xvg "
+.BI "-runav" " runaver.xvg "
 .BI "-pi" " pull.ppa "
 .BI "-po" " pullout.ppa "
 .BI "-pd" " pull.pdo "
 .BI "-pn" " pull.ndx "
+.BI "-mtx" " nm.mtx "
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
@@ -26,9 +32,21 @@ mdrun
 .BI "-np" " int "
 .BI "-[no]v" ""
 .BI "-[no]compact" ""
+.BI "-[no]multi" ""
+.BI "-[no]glas" ""
+.BI "-[no]ionize" ""
 .SH DESCRIPTION
-The mdrun program performs Molecular Dynamics simulations.
-It reads the run input file (
+The mdrun program is the main computational chemistry engine
+within GROMACS. Obviously, it performs Molecular Dynamics simulations,
+but it can also perform Brownian Dynamics and Langevin Dynamics
+as well as Conjugate Gradient or Steepest Descents energy minimization.
+Normal mode analysis is another option. In this case mdrun
+builds a Hessian matrix from single conformation.
+For usual Normal Modes-like calculations, make sure that
+the structure provided is properly energy-minimised.
+The generated matrix can be diagonalized by g_nmeig.
+
+The mdrun program reads the run input file (
 .B -s
 ) and distributes the
 topology over nodes if needed. The coordinates are passed
@@ -132,6 +150,11 @@ In both cases all the usual output will be written to file.
 When running with MPI, a signal to one of the mdrun processes
 is sufficient, this signal should not be sent to mpirun or
 the mdrun process that is the parent of the others.
+Finally some experimental algorithms can be tested when the
+appropriate options have been given. Currently under
+investigation are: polarizibility, glass simulations, 
+Free energy perturbation, X-Ray bombardments
+and parallel independent simulations.
 .SH FILES
 .BI "-s" " topol.tpr" 
 .B Input
@@ -177,6 +200,26 @@ the mdrun process that is the parent of the others.
 .B Output, Opt.
  ED sampling output 
 
+.BI "-j" " wham.gct" 
+.B Input, Opt.
+ General coupling stuff 
+
+.BI "-jo" " bam.gct" 
+.B Input, Opt.
+ General coupling stuff 
+
+.BI "-ffout" " gct.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-devout" " deviatie.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
+.BI "-runav" " runaver.xvg" 
+.B Output, Opt.
+ xvgr/xmgr file 
+
 .BI "-pi" " pull.ppa" 
 .B Input, Opt.
  Pull parameters 
@@ -193,6 +236,10 @@ the mdrun process that is the parent of the others.
 .B Input, Opt.
  Index file 
 
+.BI "-mtx" " nm.mtx" 
+.B Output, Opt.
+ Hessian matrix 
+
 .SH OTHER OPTIONS
 .BI "-[no]h"  "    no"
  Print help info and quit
@@ -215,3 +262,12 @@ the mdrun process that is the parent of the others.
 .BI "-[no]compact"  "   yes"
  Write a compact log file
 
+.BI "-[no]multi"  "    no"
+ Do multiple simulations in parallel (only with -np  1)
+
+.BI "-[no]glas"  "    no"
+ Do glass simulation with special long range corrections
+
+.BI "-[no]ionize"  "    no"
+ Do a simulation including the effect of an X-Ray bombardment on your system
+

diff --git a/man/man1/mk_angndx.1 b/man/man1/mk_angndx.1
index 103e4fbcf0912b348dfcd13b394966ab12862456..486194979d1dcccbd099730a3a5aed8e773ed797 100644 (file)
--- a/man/man1/mk_angndx.1
+++ b/man/man1/mk_angndx.1
@@ -1,7 +1,7 @@
-.TH mk_angndx 1 "Mon 23 Jul 2001"
+.TH mk_angndx 1 "Wed 27 Feb 2002"
 .SH NAME
 mk_angndx
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3mk_angndx\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/ngmx.1 b/man/man1/ngmx.1
index eac673da54c3fd41ad3bf3d6d498b83f3569839a..162d3dc815e559be1d4efed17afd01932231aabf 100644 (file)
--- a/man/man1/ngmx.1
+++ b/man/man1/ngmx.1
@@ -1,7 +1,7 @@
-.TH ngmx 1 "Mon 23 Jul 2001"
+.TH ngmx 1 "Wed 27 Feb 2002"
 .SH NAME
 ngmx
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3ngmx\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/pdb2gmx.1 b/man/man1/pdb2gmx.1
index 09d298882986774e081d0a29f26649279960d9fe..a35718ebd9f6a2b0d655a472795c026d2bad4f47 100644 (file)
--- a/man/man1/pdb2gmx.1
+++ b/man/man1/pdb2gmx.1
@@ -1,7 +1,7 @@
-.TH pdb2gmx 1 "Mon 23 Jul 2001"
+.TH pdb2gmx 1 "Wed 27 Feb 2002"
 .SH NAME
 pdb2gmx
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3pdb2gmx\fP
 .BI "-f" " eiwit.pdb "
@@ -23,6 +23,7 @@ pdb2gmx
 .BI "-[no]his" ""
 .BI "-angle" " real "
 .BI "-dist" " real "
+.BI "-posrefc" " real "
 .BI "-[no]una" ""
 .BI "-[no]sort" ""
 .BI "-[no]H14" ""
@@ -204,6 +205,9 @@ Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
 .BI "-dist"  " real" "    0.3" 
  Maximum donor-acceptor distance for a H-bond (nm)
 
+.BI "-posrefc"  " real" "   1000" 
+ Force constant for position restraints
+
 .BI "-[no]una"  "    no"
  Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine
 

diff --git a/man/man1/protonate.1 b/man/man1/protonate.1
index 8dd915bcede0ad792e6c5c71d0e1a55b867ea27a..86de7ded2cd952791a54f06ca686448734119699 100644 (file)
--- a/man/man1/protonate.1
+++ b/man/man1/protonate.1
@@ -1,7 +1,7 @@
-.TH protonate 1 "Mon 23 Jul 2001"
+.TH protonate 1 "Wed 27 Feb 2002"
 .SH NAME
 protonate
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3protonate\fP
 .BI "-s" " topol.tpr "

diff --git a/man/man1/tpbconv.1 b/man/man1/tpbconv.1
index ed978c191ffeab6549035e1af1ae57c97053cf1f..115e15629bb8030a0dc188f65361ea74b3be3e13 100644 (file)
--- a/man/man1/tpbconv.1
+++ b/man/man1/tpbconv.1
@@ -1,7 +1,7 @@
-.TH tpbconv 1 "Mon 23 Jul 2001"
+.TH tpbconv 1 "Wed 27 Feb 2002"
 .SH NAME
 tpbconv
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3tpbconv\fP
 .BI "-s" " topol.tpr "
@@ -14,9 +14,10 @@ tpbconv
 .BI "-time" " real "
 .BI "-extend" " real "
 .BI "-until" " real "
+.BI "-[no]zeroq" ""
 .BI "-[no]unconstrained" ""
 .SH DESCRIPTION
-tpbconv can edit run input files in two ways.
+tpbconv can edit run input files in three ways.
 
 
 .B 1st.
@@ -36,6 +37,11 @@ your tpx file, or when you want to make e.g. a pure Ca tpx file.
 
 .B WARNING: this tpx file is not fully functional
 .
+
+.B 3rd.
+by setting the charges of a specified group
+to zero. This is useful when doing free energy estimates
+using the LIE (Linear Interactio Energy) method.
 .SH FILES
 .BI "-s" " topol.tpr" 
 .B Input
@@ -72,6 +78,9 @@ your tpx file, or when you want to make e.g. a pure Ca tpx file.
 .BI "-until"  " real" "      0" 
  Extend runtime until this ending time (ps)
 
+.BI "-[no]zeroq"  "    no"
+ Set the charges of a group (from the index) to zero
+
 .BI "-[no]unconstrained"  "   yes"
  For a continuous trajectory, the constraints should not be solved before the first step (default)
 

diff --git a/man/man1/trjcat.1 b/man/man1/trjcat.1
index b9fbfe6f034e66fe265c10ea66154b18a0db6f73..5e903df5b5d0f0575b78303b865cc08da1ad886d 100644 (file)
--- a/man/man1/trjcat.1
+++ b/man/man1/trjcat.1
@@ -1,7 +1,7 @@
-.TH trjcat 1 "Mon 23 Jul 2001"
+.TH trjcat 1 "Wed 27 Feb 2002"
 .SH NAME
 trjcat
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3trjcat\fP
 .BI "-o" " trajout.xtc "
@@ -9,13 +9,15 @@ trjcat
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
-.BI "-b" " real "
-.BI "-e" " real "
-.BI "-dt" " real "
+.BI "-tu" " enum "
+.BI "-b" " time "
+.BI "-e" " time "
+.BI "-dt" " time "
 .BI "-prec" " int "
 .BI "-[no]vel" ""
 .BI "-[no]settime" ""
 .BI "-[no]sort" ""
+.BI "-[no]cat" ""
 .SH DESCRIPTION
 trjcat concatenates several input trajectory files in sorted order. 
 In case of double time frames the one in the later file is used. 
@@ -26,7 +28,10 @@ of each file. The input files are taken from the command line,
 such that a command like 
 .B trjcat -o fixed.trr *.trr
 should do 
-the trick.
+the trick. Using 
+.B -cat
+you can simply paste several files 
+together without removal of frames with identical time stamps.
 .SH FILES
 .BI "-o" " trajout.xtc" 
 .B Output
@@ -46,14 +51,33 @@ the trick.
 .BI "-nice"  " int" " 19" 
  Set the nicelevel
 
-.BI "-b"  " real" "     -1" 
- First time to use
+.BI "-tu"  " enum" " ps" 
+ Time unit: 
+.B ps
+, 
+.B fs
+, 
+.B ns
+, 
+.B us
+, 
+.B ms
+, 
+.B s
+, 
+.B m
+or 
+.B h
 
-.BI "-e"  " real" "     -1" 
- Last time to use
 
-.BI "-dt"  " real" "      0" 
- Only write frame when t MOD dt = first time
+.BI "-b"  " time" "     -1" 
+ First time to use (ps)
+
+.BI "-e"  " time" "     -1" 
+ Last time to use (ps)
+
+.BI "-dt"  " time" "      0" 
+ Only write frame when t MOD dt = first time (ps)
 
 .BI "-prec"  " int" " 3" 
  Precision for .xtc and .gro writing in number of decimal places
@@ -67,3 +91,6 @@ the trick.
 .BI "-[no]sort"  "   yes"
  Sort trajectory files (not frames)
 
+.BI "-[no]cat"  "    no"
+ do not discard double time frames
+

diff --git a/man/man1/trjconv.1 b/man/man1/trjconv.1
index 972d125e12e46ce247d457ac7c9221e488dbfe2d..ceb6d573b10468178b3cb0c832bbb1be03eb05ce 100644 (file)
--- a/man/man1/trjconv.1
+++ b/man/man1/trjconv.1
@@ -1,7 +1,7 @@
-.TH trjconv 1 "Mon 23 Jul 2001"
+.TH trjconv 1 "Wed 27 Feb 2002"
 .SH NAME
 trjconv
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3trjconv\fP
 .BI "-f" " traj.xtc "
@@ -146,6 +146,12 @@ append output to an existing trajectory file.
 No checks are performed to ensure integrity
 of the resulting combined trajectory file.
 
+
+Option 
+.B -sep
+can be used to write every frame to a seperate
+.gro, .g96 or .pdb file, default all frames all written to one file.
+
 .B .pdb
 files with all frames concatenated can be viewed with
 
@@ -404,5 +410,5 @@ or
  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
+ Write each frame to a separate .gro, .g96 or .pdb file
 

diff --git a/man/man1/trjorder.1 b/man/man1/trjorder.1
index f79b2847e84e18b593cb13e01964c03a28a577d5..e8ff3c9be02cef6be463669bda85cab68f73b68e 100644 (file)
--- a/man/man1/trjorder.1
+++ b/man/man1/trjorder.1
@@ -1,7 +1,7 @@
-.TH trjorder 1 "Mon 23 Jul 2001"
+.TH trjorder 1 "Wed 27 Feb 2002"
 .SH NAME
 trjorder
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3trjorder\fP
 .BI "-f" " traj.xtc "

diff --git a/man/man1/wheel.1 b/man/man1/wheel.1
index 6c54d3857163ae5e78ca710b24409c893e1a2335..ad6398561c0a6a42c6f3090919e3f5348b01fcfd 100644 (file)
--- a/man/man1/wheel.1
+++ b/man/man1/wheel.1
@@ -1,7 +1,7 @@
-.TH wheel 1 "Mon 23 Jul 2001"
+.TH wheel 1 "Wed 27 Feb 2002"
 .SH NAME
 wheel
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3wheel\fP
 .BI "-f" " nnnice.dat "

diff --git a/man/man1/x2top.1 b/man/man1/x2top.1
index c9897dee7b94b4d4eba62b95ccdbe93ad9225db1..2dedb81e83ec91449af9949c733585fae5f1db32 100644 (file)
--- a/man/man1/x2top.1
+++ b/man/man1/x2top.1
@@ -1,7 +1,7 @@
-.TH x2top 1 "Mon 23 Jul 2001"
+.TH x2top 1 "Wed 27 Feb 2002"
 .SH NAME
 x2top
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3x2top\fP
 .BI "-f" " conf.gro "
@@ -10,21 +10,33 @@ x2top
 .BI "-[no]h" ""
 .BI "-[no]X" ""
 .BI "-nice" " int "
-.BI "-kb" " real "
-.BI "-kt" " real "
-.BI "-kp" " real "
+.BI "-scale" " real "
 .BI "-nexcl" " int "
 .BI "-[no]H14" ""
 .BI "-[no]alldih" ""
-.BI "-[no]round" ""
 .BI "-[no]pairs" ""
 .BI "-name" " string "
+.BI "-[no]pbc" ""
+.BI "-[no]param" ""
+.BI "-[no]round" ""
+.BI "-kb" " real "
+.BI "-kt" " real "
+.BI "-kp" " real "
 .SH DESCRIPTION
 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.
 The program can also make an rtp entry, which you can then add
 to the rtp database.
+
+
+When 
+.B -param
+is set, equilibrium distances and angles
+and force constants will be printed in the topology for all
+interactions. The equilibrium distances and angles are taken
+from the input coordinates, the force constant are set with
+command line options.
 .SH FILES
 .BI "-f" " conf.gro" 
 .B Input
@@ -48,14 +60,8 @@ to the rtp database.
 .BI "-nice"  " int" " 0" 
  Set the nicelevel
 
-.BI "-kb"  " real" " 400000" 
- Bonded force constant (kJ/mol/nm2)
-
-.BI "-kt"  " real" "    400" 
- Angle force constant (kJ/mol/rad2)
-
-.BI "-kp"  " real" "      5" 
- Dihedral angle force constant (kJ/mol/rad2)
+.BI "-scale"  " real" "    1.1" 
+ Scaling factor for bonds with unknown atom types relative to atom type O
 
 .BI "-nexcl"  " int" " 3" 
  Number of exclusions
@@ -66,15 +72,30 @@ to the rtp database.
 .BI "-[no]alldih"  "    no"
  Generate all proper dihedrals
 
-.BI "-[no]round"  "   yes"
- Round off measured values
-
 .BI "-[no]pairs"  "   yes"
  Output 1-4 interactions (pairs) in topology file
 
 .BI "-name"  " string" " ICE" 
  Name of your molecule
 
+.BI "-[no]pbc"  "   yes"
+ Use periodic boundary conditions. Please set the GMXFULLPBC environment variable as well.
+
+.BI "-[no]param"  "    no"
+ Print parameters in the output
+
+.BI "-[no]round"  "   yes"
+ Round off measured values
+
+.BI "-kb"  " real" " 400000" 
+ Bonded force constant (kJ/mol/nm2)
+
+.BI "-kt"  " real" "    400" 
+ Angle force constant (kJ/mol/rad2)
+
+.BI "-kp"  " real" "      5" 
+ Dihedral angle force constant (kJ/mol/rad2)
+
 \- The atom type selection is primitive. Virtually no chemical knowledge is used
 
 \- Periodic boundary conditions screw up the bonding

diff --git a/man/man1/xpm2ps.1 b/man/man1/xpm2ps.1
index 891b5c12ac1498682e30f4d7ed6bd3570f90ad54..ecfcc7a7773056741b7dadd1e3156a7432f276a3 100644 (file)
--- a/man/man1/xpm2ps.1
+++ b/man/man1/xpm2ps.1
@@ -1,7 +1,7 @@
-.TH xpm2ps 1 "Mon 23 Jul 2001"
+.TH xpm2ps 1 "Wed 27 Feb 2002"
 .SH NAME
 xpm2ps
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3xpm2ps\fP
 .BI "-f" " root.xpm "

diff --git a/man/man1/xrama.1 b/man/man1/xrama.1
index 155afd057a6b5a116162a1022a6ce93fc9898b1f..396217173adb61219fd4206d87107d114e4b5859 100644 (file)
--- a/man/man1/xrama.1
+++ b/man/man1/xrama.1
@@ -1,7 +1,7 @@
-.TH xrama 1 "Mon 23 Jul 2001"
+.TH xrama 1 "Wed 27 Feb 2002"
 .SH NAME
 xrama
-.B VERSION 3.0
+.B VERSION 3.1.beta_20020215
 .SH SYNOPSIS
 \f3xrama\fP
 .BI "-f" " traj.xtc "

diff --git a/scripts/completion.bash b/scripts/completion.bash
index 1d5680e744704b52aefa01d5a8069b6373dc511e..daed499392cee35b4447696c49423838d7c8d0cf 100644 (file)
--- a/scripts/completion.bash
+++ b/scripts/completion.bash
@@ -15,7 +15,7 @@ case "$p" in
 -a) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ta) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -aa) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _do_dssp_compl do_dssp
 shopt -s extglob
 _editconf_compl() {
@@ -28,7 +28,7 @@ case "$p" in
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -bf) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _editconf_compl editconf
 shopt -s extglob
 _eneconv_compl() {
@@ -38,9 +38,22 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _eneconv_compl eneconv
 shopt -s extglob
+_ffscan_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -g -table -parm -ga -h -X -nice -tol -fmax -epot -nocomb -npow -ratio -logeps -nov' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-table) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-parm) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ga) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _ffscan_compl ffscan
+shopt -s extglob
 _g_anaeig_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -62,17 +75,17 @@ case "$p" in
 -extr) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -over) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -inpr) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_anaeig_compl g_anaeig
 shopt -s extglob
 _g_analyze_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -ac -msd -cc -dist -av -ee -h -X -nice -w -notime -b -e -n -d -bw -errbar -power -nosubav -oneacf -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -ac -msd -cc -dist -av -ee -g -h -X -nice -w -notime -b -e -n -d -bw -errbar -power -nosubav -oneacf -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
 case "$p" in
 -errbar) COMPREPLY=( $(compgen -W ' none stddev error 90 ' -- $c ));;
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ac) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -msd) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -80,7 +93,8 @@ case "$p" in
 -dist) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -av) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ee) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
 complete -F _g_analyze_compl g_analyze
 shopt -s extglob
 _g_angle_compl() {
@@ -90,7 +104,7 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -type) COMPREPLY=( $(compgen -W ' angle dihedral improper ryckaert-bellemans ' -- $c ));;
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -100,19 +114,21 @@ case "$p" in
 -ot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oh) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_angle_compl g_angle
 shopt -s extglob
 _g_bond_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -n -o -l -h -X -nice -b -e -dt -w -blen -tol -noaver' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -n -s -o -l -d -h -X -nice -b -e -dt -w -blen -tol -noaver' -- $c)); return 0; fi
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+-d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
 complete -F _g_bond_compl g_bond
 shopt -s extglob
 _g_bundle_compl() {
@@ -134,7 +150,7 @@ case "$p" in
 -okr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -okl) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oa) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_bundle_compl g_bundle
 shopt -s extglob
 _g_chi_compl() {
@@ -144,7 +160,7 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -c
 case "$p" in
 -maxchi) COMPREPLY=( $(compgen -W ' 0 1 2 3 4 5 6 ' -- $c ));;
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -153,13 +169,13 @@ case "$p" in
 -jc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -corr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_chi_compl g_chi
 shopt -s extglob
 _g_cluster_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -dm -o -g -dist -ev -sz -tr -ntr -clid -cl -h -X -nice -b -e -dt -tu -w -dista -nlevels -keepfree -cutoff -max -skip -av -wcl -nst -rmsmin -method -binary -M -P -seed -niter -kT' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -dm -o -g -dist -ev -sz -tr -ntr -clid -cl -h -X -nice -b -e -dt -tu -w -dista -nlevels -keepfree -cutoff -nofit -max -skip -av -wcl -nst -rmsmin -method -binary -M -P -seed -niter -kT' -- $c)); return 0; fi
 case "$p" in
 -tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
 -method) COMPREPLY=( $(compgen -W ' linkage jarvis-patrick monte-carlo diagonalization gromos ' -- $c ));;
@@ -176,9 +192,23 @@ case "$p" in
 -ntr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -clid) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -cl) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_cluster_compl g_cluster
 shopt -s extglob
+_g_clustsize_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -n -o -nc -mc -ac -h -X -nice -b -e -dt -w -cut -nskip -nlevels -rgblo -rgbhi' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-nc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-mc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ac) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _g_clustsize_compl g_clustsize
+shopt -s extglob
 _g_confrms_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -189,7 +219,7 @@ case "$p" in
 -o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n1) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n2) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_confrms_compl g_confrms
 shopt -s extglob
 _g_covar_compl() {
@@ -207,7 +237,7 @@ case "$p" in
 -l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -xpm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -xpma) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_covar_compl g_covar
 shopt -s extglob
 _g_density_compl() {
@@ -220,7 +250,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ei) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_density_compl g_density
 shopt -s extglob
 _g_dielectric_compl() {
@@ -228,12 +258,12 @@ local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
 if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -d -o -c -h -X -nice -b -e -dt -w -fft -nox1 -eint -bfit -efit -tail -A -tau1 -tau2 -eps0 -epsRF -fix -ffn -nsmooth' -- $c)); return 0; fi
 case "$p" in
--ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-ffn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -d) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -c) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_dielectric_compl g_dielectric
 shopt -s extglob
 _g_dih_compl() {
@@ -244,7 +274,7 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_dih_compl g_dih
 shopt -s extglob
 _g_dipoles_compl() {
@@ -253,7 +283,7 @@ COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
 if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -enx -f -s -n -o -e -a -d -c -g -q -h -X -nice -b -e -dt -w -mu -mumax -epsilonRF -skip -temp -avercorr -gkratom -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
 case "$p" in
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -enx) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -265,7 +295,7 @@ case "$p" in
 -c) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -g) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -q) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_dipoles_compl g_dipoles
 shopt -s extglob
 _g_disre_compl() {
@@ -282,7 +312,7 @@ case "$p" in
 -dr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -l) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_disre_compl g_disre
 shopt -s extglob
 _g_dist_compl() {
@@ -294,7 +324,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_dist_compl g_dist
 shopt -s extglob
 _g_dyndom_compl() {
@@ -305,9 +335,33 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_dyndom_compl g_dyndom
 shopt -s extglob
+_genbox_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -cp -cs -ci -o -p -h -X -nice -box -nmol -try -seed -vdwd -shell' -- $c)); return 0; fi
+case "$p" in
+-cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _genbox_compl genbox
+shopt -s extglob
+_genconf_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -trj -h -X -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -renumber' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _genconf_compl genconf
+shopt -s extglob
 _g_enemat_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -318,28 +372,57 @@ case "$p" in
 -eref) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -emat) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -etot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_enemat_compl g_enemat
 shopt -s extglob
 _g_energy_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -f2 -s -o -viol -pairs -corr -vis -ravg -h -X -nice -b -e -w -fee -fetemp -zero -sum -dp -mutot -skip -aver -nmol -ndf -fluc -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -f2 -s -o -viol -pairs -ora -ort -oda -odr -odt -corr -vis -ravg -h -X -nice -b -e -w -fee -fetemp -zero -sum -dp -mutot -skip -aver -nmol -ndf -fluc -orinst -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
 case "$p" in
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -f2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -viol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -pairs) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ora) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ort) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-oda) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-odr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-odt) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -corr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -vis) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ravg) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_energy_compl g_energy
 shopt -s extglob
+_genion_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -n -o -g -pot -h -X -nice -np -pname -pq -nn -nname -nq -rmin -random -seed' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-pot) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _genion_compl genion
+shopt -s extglob
+_genpr_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -n -o -h -X -nice -fc' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _genpr_compl genpr
+shopt -s extglob
 _g_gyrate_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -349,7 +432,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_gyrate_compl g_gyrate
 shopt -s extglob
 _g_h2order_compl() {
@@ -362,7 +445,7 @@ case "$p" in
 -nm) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_h2order_compl g_h2order
 shopt -s extglob
 _g_hbond_compl() {
@@ -383,7 +466,7 @@ case "$p" in
 -hbn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -hbm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -da) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_hbond_compl g_hbond
 shopt -s extglob
 _g_helix_compl() {
@@ -397,7 +480,7 @@ case "$p" in
 -to) COMPREPLY=( $(compgen -X '!*.g87*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -cz) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -co) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_helix_compl g_helix
 shopt -s extglob
 _g_lie_compl() {
@@ -407,7 +490,7 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_lie_compl g_lie
 shopt -s extglob
 _g_mdmat_compl() {
@@ -421,7 +504,7 @@ case "$p" in
 -mean) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -frames) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -no) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_mdmat_compl g_mdmat
 shopt -s extglob
 _g_mindist_compl() {
@@ -435,7 +518,7 @@ case "$p" in
 -od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -on) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.out*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_mindist_compl g_mindist
 shopt -s extglob
 _g_morph_compl() {
@@ -448,7 +531,7 @@ case "$p" in
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -or) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_morph_compl g_morph
 shopt -s extglob
 _g_msd_compl() {
@@ -464,9 +547,35 @@ case "$p" in
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -mol) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_msd_compl g_msd
 shopt -s extglob
+_gmxcheck_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -f2 -s1 -s2 -c -e -e2 -h -X -nice -vdwfac -bonlo -bonhi -tol -lastener' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-s2) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _gmxcheck_compl gmxcheck
+shopt -s extglob
+_gmxdump_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -f -e -h -X -nice -nonr' -- $c)); return 0; fi
+case "$p" in
+-s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _gmxdump_compl gmxdump
+shopt -s extglob
 _g_nmeig_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -476,7 +585,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -v) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_nmeig_compl g_nmeig
 shopt -s extglob
 _g_nmens_compl() {
@@ -489,7 +598,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_nmens_compl g_nmens
 shopt -s extglob
 _g_order_compl() {
@@ -504,7 +613,7 @@ case "$p" in
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -os) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_order_compl g_order
 shopt -s extglob
 _g_potential_compl() {
@@ -518,7 +627,7 @@ case "$p" in
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_potential_compl g_potential
 shopt -s extglob
 _g_rama_compl() {
@@ -529,7 +638,7 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rama_compl g_rama
 shopt -s extglob
 _g_rdf_compl() {
@@ -545,7 +654,7 @@ case "$p" in
 -cn) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -hq) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -image) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rdf_compl g_rdf
 shopt -s extglob
 _g_rms_compl() {
@@ -566,7 +675,7 @@ case "$p" in
 -m) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -bin) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -bm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rms_compl g_rms
 shopt -s extglob
 _g_rmsdist_compl() {
@@ -585,7 +694,7 @@ case "$p" in
 -nmr3) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -nmr6) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -noe) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rmsdist_compl g_rmsdist
 shopt -s extglob
 _g_rmsf_compl() {
@@ -603,21 +712,39 @@ case "$p" in
 -od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -dir) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rmsf_compl g_rmsf
 shopt -s extglob
+_grompp_compl() {
+local p c
+COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -po -c -r -n -deshuf -p -pp -o -t -h -X -nice -nov -time -np -shuffle -sort -normdumbds -load -maxwarn -check14' -- $c)); return 0; fi
+case "$p" in
+-f) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-po) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-deshuf) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-pp) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-t) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
+complete -F _grompp_compl grompp
+shopt -s extglob
 _g_rotacf_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
 if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -o -h -X -nice -b -e -dt -w -d -noaver -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
 case "$p" in
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_rotacf_compl g_rotacf
 shopt -s extglob
 _g_saltbr_compl() {
@@ -627,13 +754,13 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_saltbr_compl g_saltbr
 shopt -s extglob
 _g_sas_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -o -r -q -ao -n -i -h -X -nice -b -e -dt -w -solsize -ndots -qmax -minarea -skip -noprot' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -o -r -q -ao -n -i -h -X -nice -b -e -dt -w -solsize -ndots -qmax -minarea -skip -nopbc -noprot -dgs' -- $c)); return 0; fi
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -643,7 +770,7 @@ case "$p" in
 -ao) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -i) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_sas_compl g_sas
 shopt -s extglob
 _g_sgangle_compl() {
@@ -658,7 +785,7 @@ case "$p" in
 -od) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -od1) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -od2) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_sgangle_compl g_sgangle
 shopt -s extglob
 _g_sorient_compl() {
@@ -673,7 +800,7 @@ case "$p" in
 -no) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ro) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -co) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_sorient_compl g_sorient
 shopt -s extglob
 _g_tcaf_compl() {
@@ -690,13 +817,13 @@ case "$p" in
 -of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -oc) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ov) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_tcaf_compl g_tcaf
 shopt -s extglob
 _g_traj_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -ox -ov -of -ob -ot -ekr -h -X -nice -b -e -dt -tu -w -com -mol -nojump -nox -noy -noz -len' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -ox -ov -of -ob -ot -ekt -ekr -cv -cf -h -X -nice -b -e -dt -tu -w -com -mol -nojump -nox -noy -noz -len' -- $c)); return 0; fi
 case "$p" in
 -tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -707,8 +834,11 @@ case "$p" in
 -of) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ob) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ot) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ekt) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ekr) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+-cv) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-cf) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
 complete -F _g_traj_compl g_traj
 shopt -s extglob
 _g_velacc_compl() {
@@ -717,106 +847,14 @@ COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
 if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -s -n -o -h -X -nice -b -e -dt -w -mol -acflen -nonormalize -P -fitfn -ncskip -beginfit -endfit' -- $c)); return 0; fi
 case "$p" in
 -P) COMPREPLY=( $(compgen -W ' 0 1 2 3 ' -- $c ));;
--fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac ' -- $c ));;
+-fitfn) COMPREPLY=( $(compgen -W ' none exp aexp exp_exp vac exp5 exp7 ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _g_velacc_compl g_velacc
 shopt -s extglob
-_genbox_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -cp -cs -ci -o -p -h -X -nice -box -nmol -try -seed -vdwd -shell' -- $c)); return 0; fi
-case "$p" in
--cp) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--cs) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ci) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genbox_compl genbox
-shopt -s extglob
-_genconf_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -trj -h -X -nice -nbox -dist -seed -rot -shuffle -sort -block -nmolat -maxrot -renumber' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--trj) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genconf_compl genconf
-shopt -s extglob
-_genion_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -n -o -g -pot -h -X -nice -np -pname -pq -nn -nname -nq -rmin -random -seed' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pot) COMPREPLY=( $(compgen -X '!*.pdb*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genion_compl genion
-shopt -s extglob
-_genpr_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -n -o -h -X -nice -fc' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _genpr_compl genpr
-shopt -s extglob
-_gmxcheck_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -f2 -s1 -s2 -c -e -e2 -h -X -nice -vdwfac -bonlo -bonhi -tol' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f2) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s1) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--s2) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e2) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _gmxcheck_compl gmxcheck
-shopt -s extglob
-_gmxdump_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -f -e -h -X -nice -nonr' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _gmxdump_compl gmxdump
-shopt -s extglob
-_grompp_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -po -c -r -n -deshuf -p -pp -o -t -h -X -nice -nov -time -np -shuffle -sort -normdumbds -load -maxwarn -check14' -- $c)); return 0; fi
-case "$p" in
--f) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--po) COMPREPLY=( $(compgen -X '!*.mdp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--r) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--deshuf) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--p) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pp) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--t) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _grompp_compl grompp
-shopt -s extglob
 _highway_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -824,7 +862,7 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -a) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _highway_compl highway
 shopt -s extglob
 _make_ndx_compl() {
@@ -835,13 +873,13 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _make_ndx_compl make_ndx
 shopt -s extglob
 _mdrun_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -o -x -c -e -g -dgdl -table -rerun -ei -eo -pi -po -pd -pn -h -X -nice -deffnm -np -v -nocompact' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -o -x -c -e -g -dgdl -table -rerun -ei -eo -j -jo -ffout -devout -runav -pi -po -pd -pn -mtx -h -X -nice -deffnm -np -v -nocompact -multi -glas -ionize' -- $c)); return 0; fi
 case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -854,11 +892,17 @@ case "$p" in
 -rerun) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -ei) COMPREPLY=( $(compgen -X '!*.edi*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -eo) COMPREPLY=( $(compgen -X '!*.edo*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-j) COMPREPLY=( $(compgen -X '!*.gct*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-jo) COMPREPLY=( $(compgen -X '!*.gct*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-ffout) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-devout) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+-runav) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -pi) COMPREPLY=( $(compgen -X '!*.ppa*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -po) COMPREPLY=( $(compgen -X '!*.ppa*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -pd) COMPREPLY=( $(compgen -X '!*.pdo*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -pn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+-mtx) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
+esac; }; 
 complete -F _mdrun_compl mdrun
 shopt -s extglob
 _mk_angndx_compl() {
@@ -869,7 +913,7 @@ case "$p" in
 -type) COMPREPLY=( $(compgen -W ' angle g96-angle dihedral improper ryckaert-bellemans phi-psi ' -- $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _mk_angndx_compl mk_angndx
 shopt -s extglob
 _ngmx_compl() {
@@ -880,24 +924,13 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _ngmx_compl ngmx
 shopt -s extglob
-_nmrun_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -m -g -h -X -nice -np -v -nocompact' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--m) COMPREPLY=( $(compgen -X '!*.mtx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _nmrun_compl nmrun
-shopt -s extglob
 _pdb2gmx_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -p -i -n -q -h -X -nice -merge -inter -ss -ter -lys -asp -glu -his -angle -dist -una -nosort -H14 -ignh -alldih -dummy -heavyh -deuterate' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -p -i -n -q -h -X -nice -merge -inter -ss -ter -lys -asp -glu -his -angle -dist -posrefc -una -nosort -H14 -ignh -alldih -dummy -heavyh -deuterate' -- $c)); return 0; fi
 case "$p" in
 -dummy) COMPREPLY=( $(compgen -W ' none hydrogens aromatics ' -- $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
@@ -906,7 +939,7 @@ case "$p" in
 -i) COMPREPLY=( $(compgen -X '!*.itp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -q) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _pdb2gmx_compl pdb2gmx
 shopt -s extglob
 _protonate_compl() {
@@ -918,29 +951,30 @@ case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _protonate_compl protonate
 shopt -s extglob
 _tpbconv_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -f -n -o -h -X -nice -time -extend -until -nounconstrained' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -f -n -o -h -X -nice -time -extend -until -zeroq -nounconstrained' -- $c)); return 0; fi
 case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -f) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _tpbconv_compl tpbconv
 shopt -s extglob
 _trjcat_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -o -n -h -X -nice -b -e -dt -prec -novel -settime -nosort' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -o -n -h -X -nice -tu -b -e -dt -prec -novel -settime -nosort -cat' -- $c)); return 0; fi
 case "$p" in
+-tu) COMPREPLY=( $(compgen -W ' ps fs ns us ms s m h ' -- $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _trjcat_compl trjcat
 shopt -s extglob
 _trjconv_compl() {
@@ -956,7 +990,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -fr) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _trjconv_compl trjconv
 shopt -s extglob
 _trjorder_compl() {
@@ -968,7 +1002,7 @@ case "$p" in
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa|gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -n) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _trjorder_compl trjorder
 shopt -s extglob
 _wheel_compl() {
@@ -978,48 +1012,20 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.dat*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.eps*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _wheel_compl wheel
 shopt -s extglob
 _x2top_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -r -h -X -nice -kb -kt -kp -nexcl -H14 -alldih -noround -nopairs -name' -- $c)); return 0; fi
+if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f -o -r -h -X -nice -scale -nexcl -H14 -alldih -nopairs -name -nopbc -param -noround -kb -kt -kp' -- $c)); return 0; fi
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent|tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.top*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -r) COMPREPLY=( $(compgen -X '!*.rtp*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _x2top_compl x2top
 shopt -s extglob
-_xmdrun_compl() {
-local p c
-COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
-if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -s -o -x -c -e -g -dgdl -table -rerun -ei -eo -j -jo -ffout -devout -runav -pi -po -pd -pn -h -X -nice -deffnm -np -v -nocompact -multi -glas -ionize' -- $c)); return 0; fi
-case "$p" in
--s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--o) COMPREPLY=( $(compgen -X '!*.+(trr|trj)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--x) COMPREPLY=( $(compgen -X '!*.xtc*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--c) COMPREPLY=( $(compgen -X '!*.+(gro|g96|pdb|brk|ent)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--e) COMPREPLY=( $(compgen -X '!*.+(edr|ene)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--g) COMPREPLY=( $(compgen -X '!*.log*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--dgdl) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--table) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--rerun) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ei) COMPREPLY=( $(compgen -X '!*.edi*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--eo) COMPREPLY=( $(compgen -X '!*.edo*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--j) COMPREPLY=( $(compgen -X '!*.gct*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--jo) COMPREPLY=( $(compgen -X '!*.gct*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--ffout) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--devout) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--runav) COMPREPLY=( $(compgen -X '!*.xvg*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pi) COMPREPLY=( $(compgen -X '!*.ppa*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--po) COMPREPLY=( $(compgen -X '!*.ppa*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pd) COMPREPLY=( $(compgen -X '!*.pdo*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
--pn) COMPREPLY=( $(compgen -X '!*.ndx*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
-complete -F _xmdrun_compl xmdrun
-shopt -s extglob
 _xpm2ps_compl() {
 local p c
 COMPREPLY=() c=${COMP_WORDS[COMP_CWORD]} p=${COMP_WORDS[COMP_CWORD-1]}
@@ -1036,7 +1042,7 @@ case "$p" in
 -do) COMPREPLY=( $(compgen -X '!*.m2p*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -o) COMPREPLY=( $(compgen -X '!*.eps*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -xpm) COMPREPLY=( $(compgen -X '!*.xpm*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _xpm2ps_compl xpm2ps
 shopt -s extglob
 _xrama_compl() {
@@ -1046,5 +1052,5 @@ if (( $COMP_CWORD <= 1 )) || [[ $c == -* ]]; then COMPREPLY=( $(compgen  -W ' -f
 case "$p" in
 -f) COMPREPLY=( $(compgen -X '!*.+(xtc|trr|trj|gro|g96|pdb|g87)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
 -s) COMPREPLY=( $(compgen -X '!*.+(tpr|tpb|tpa)*(.gz|.Z)' -f $c ; compgen -S '/' -X '.*' -d $c ));;
-esac }
+esac; }; 
 complete -F _xrama_compl xrama

diff --git a/scripts/completion.csh b/scripts/completion.csh
index 9769d36d55f1084edb29e34b433dcb7c0bb2ce91..0de7571622ebaa9703d2a436f0d26718776a7a58 100644 (file)
--- a/scripts/completion.csh
+++ b/scripts/completion.csh
@@ -1,24 +1,30 @@
 complete do_dssp "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ssdump/f:*.dat{,.gz,.Z}/" "n/-map/f:*.map{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-sc/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xpm{,.gz,.Z}/" "n/-ta/f:*.xvg{,.gz,.Z}/" "n/-aa/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ssdump map o sc a ta aa h X nice b e dt tu w sss)/"
 complete editconf "n/-bt/( tric cubic dodecahedron octahedron)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-bf/f:*.dat{,.gz,.Z}/" "c/-/( f n o bf h X nice w ndef bt box angles d c center rotate princ scale density pbc mead grasp rvdw atom legend label)/"
 complete eneconv "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-o/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f o h X nice b e dt offset settime nosort scalefac noerror)/"
+complete ffscan "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-parm/f:*.dat{,.gz,.Z}/" "n/-ga/f:*.dat{,.gz,.Z}/" "c/-/( s g table parm ga h X nice tol fmax epot nocomb npow ratio logeps nov)/"
 complete g_anaeig "n/-tu/( ps fs ns us ms s m h)/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-v2/f:*.{trr,trj}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-eig1/f:*.xvg{,.gz,.Z}/" "n/-eig2/f:*.xvg{,.gz,.Z}/" "n/-disp/f:*.xvg{,.gz,.Z}/" "n/-proj/f:*.xvg{,.gz,.Z}/" "n/-2d/f:*.xvg{,.gz,.Z}/" "n/-3d/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-filt/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-extr/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-over/f:*.xvg{,.gz,.Z}/" "n/-inpr/f:*.xpm{,.gz,.Z}/" "c/-/( v v2 f s n eig1 eig2 disp proj 2d 3d filt extr over inpr h X nice b e dt tu w first last skip max nframes split)/"
-complete g_analyze "n/-errbar/( none stddev error 90)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-msd/f:*.xvg{,.gz,.Z}/" "n/-cc/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-ee/f:*.xvg{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_angle "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_bond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "c/-/( f n o l h X nice b e dt w blen tol noaver)/"
+complete g_analyze "n/-errbar/( none stddev error 90)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-msd/f:*.xvg{,.gz,.Z}/" "n/-cc/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-av/f:*.xvg{,.gz,.Z}/" "n/-ee/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( f ac msd cc dist av ee g h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_angle "n/-type/( angle dihedral improper ryckaert-bellemans)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oh/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "c/-/( f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_bond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o l d h X nice b e dt w blen tol noaver)/"
 complete g_bundle "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ol/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oz/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-otr/f:*.xvg{,.gz,.Z}/" "n/-otl/f:*.xvg{,.gz,.Z}/" "n/-ok/f:*.xvg{,.gz,.Z}/" "n/-okr/f:*.xvg{,.gz,.Z}/" "n/-okl/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ol od oz ot otr otl ok okr okl oa h X nice b e dt tu na z)/"
-complete g_chi "n/-maxchi/( 0 1 2 3 4 5 6)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-p/f:*.pdb{,.gz,.Z}/" "n/-ss/f:*.dat{,.gz,.Z}/" "n/-jc/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete g_cluster "n/-tu/( ps fs ns us ms s m h)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dm/f:*.xpm{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ev/f:*.xvg{,.gz,.Z}/" "n/-sz/f:*.xvg{,.gz,.Z}/" "n/-tr/f:*.xpm{,.gz,.Z}/" "n/-ntr/f:*.xvg{,.gz,.Z}/" "n/-clid/f:*.xvg{,.gz,.Z}/" "n/-cl/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff max skip av wcl nst rmsmin method binary M P seed niter kT)/"
+complete g_chi "n/-maxchi/( 0 1 2 3 4 5 6)/" "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-p/f:*.pdb{,.gz,.Z}/" "n/-ss/f:*.dat{,.gz,.Z}/" "n/-jc/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_cluster "n/-tu/( ps fs ns us ms s m h)/" "n/-method/( linkage jarvis-patrick monte-carlo diagonalization gromos)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-dm/f:*.xpm{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ev/f:*.xvg{,.gz,.Z}/" "n/-sz/f:*.xvg{,.gz,.Z}/" "n/-tr/f:*.xpm{,.gz,.Z}/" "n/-ntr/f:*.xvg{,.gz,.Z}/" "n/-clid/f:*.xvg{,.gz,.Z}/" "n/-cl/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method binary M P seed niter kT)/"
+complete g_clustsize "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xpm{,.gz,.Z}/" "n/-nc/f:*.xvg{,.gz,.Z}/" "n/-mc/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "c/-/( f n o nc mc ac h X nice b e dt w cut nskip nlevels rgblo rgbhi)/"
 complete g_confrms "n/-f1/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n1/f:*.ndx{,.gz,.Z}/" "n/-n2/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o n1 n2 h X nice one pbc)/"
 complete g_covar "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-av/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "n/-xpma/f:*.xpm{,.gz,.Z}/" "c/-/( f s n o v av l xpm xpma h X nice b e dt tu nofit ref mwa last)/"
 complete g_density "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-ei/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n s ei o h X nice b e dt w d sl number ed count)/"
-complete g_dielectric "n/-ffn/( none exp aexp exp_exp vac)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "c/-/( f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
+complete g_dielectric "n/-ffn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "c/-/( f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth)/"
 complete g_dih "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "c/-/( f s o h X nice b e dt w sa mult)/"
-complete g_dipoles "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-enx/f:*.{edr,ene}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "c/-/( enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_dipoles "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-enx/f:*.{edr,ene}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-d/f:*.xvg{,.gz,.Z}/" "n/-c/f:*.xvg{,.gz,.Z}/" "n/-g/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.xvg{,.gz,.Z}/" "c/-/( enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit)/"
 complete g_disre "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ds/f:*.xvg{,.gz,.Z}/" "n/-da/f:*.xvg{,.gz,.Z}/" "n/-dn/f:*.xvg{,.gz,.Z}/" "n/-dm/f:*.xvg{,.gz,.Z}/" "n/-dr/f:*.xvg{,.gz,.Z}/" "n/-l/f:*.log{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s f ds da dn dm dr l n h X nice b e dt w ntop)/"
 complete g_dist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt dist)/"
 complete g_dyndom "n/-f/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f o n h X nice firstangle lastangle nframe maxangle trans head tail)/"
+complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h X nice box nmol try seed vdwd shell)/"
+complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber)/"
 complete g_enemat "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-groups/f:*.dat{,.gz,.Z}/" "n/-eref/f:*.dat{,.gz,.Z}/" "n/-emat/f:*.xpm{,.gz,.Z}/" "n/-etot/f:*.xvg{,.gz,.Z}/" "c/-/( f groups eref emat etot h X nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp)/"
-complete g_energy "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-f2/f:*.{edr,ene}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-viol/f:*.xvg{,.gz,.Z}/" "n/-pairs/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-vis/f:*.xvg{,.gz,.Z}/" "n/-ravg/f:*.xvg{,.gz,.Z}/" "c/-/( f f2 s o viol pairs corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete g_energy "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{edr,ene}{,.gz,.Z}/" "n/-f2/f:*.{edr,ene}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-viol/f:*.xvg{,.gz,.Z}/" "n/-pairs/f:*.xvg{,.gz,.Z}/" "n/-ora/f:*.xvg{,.gz,.Z}/" "n/-ort/f:*.xvg{,.gz,.Z}/" "n/-oda/f:*.xvg{,.gz,.Z}/" "n/-odr/f:*.xvg{,.gz,.Z}/" "n/-odt/f:*.xvg{,.gz,.Z}/" "n/-corr/f:*.xvg{,.gz,.Z}/" "n/-vis/f:*.xvg{,.gz,.Z}/" "n/-ravg/f:*.xvg{,.gz,.Z}/" "c/-/( f f2 s o viol pairs ora ort oda odr odt corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete genion "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "c/-/( s n o g pot h X nice np pname pq nn nname nq rmin random seed)/"
+complete genpr "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.itp{,.gz,.Z}/" "c/-/( f n o h X nice fc)/"
 complete g_gyrate "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s o n h X nice b e dt w q p)/"
 complete g_h2order "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-nm/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f n nm s o h X nice b e dt w d sl)/"
 complete g_hbond "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-sel/f:*.ndx{,.gz,.Z}/" "n/-num/f:*.xvg{,.gz,.Z}/" "n/-ac/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-ang/f:*.xvg{,.gz,.Z}/" "n/-hx/f:*.xvg{,.gz,.Z}/" "n/-hbn/f:*.ndx{,.gz,.Z}/" "n/-hbm/f:*.xpm{,.gz,.Z}/" "n/-da/f:*.xvg{,.gz,.Z}/" "c/-/( f s n g sel num ac dist ang hx hbn hbm da h X nice b e dt ins a r abin rbin nonitacc shell)/"
@@ -28,6 +34,8 @@ complete g_mdmat "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{t
 complete g_mindist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-on/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.out{,.gz,.Z}/" "c/-/( f s n od on o h X nice b e dt w matrix d pi)/"
 complete g_morph "n/-f1/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-f2/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-or/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f1 f2 o or n h X nice w ninterm first last nofit)/"
 complete g_msd "n/-tu/( ps fs ns us ms s m h)/" "n/-type/( no x y z)/" "n/-lateral/( no x y z)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mol/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o mol h X nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit)/"
+complete gmxcheck "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s1/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-s2/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-c/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-e2/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol lastener)/"
+complete gmxdump "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( s f e h X nice nonr)/"
 complete g_nmeig "n/-f/f:*.mtx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f s o v h X nice nom first last)/"
 complete g_nmens "n/-v/f:*.{trr,trj}{,.gz,.Z}/" "n/-e/f:*.xvg{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( v e s n o h X nice temp seed num first last)/"
 complete g_order "n/-d/( z x y)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-os/f:*.xvg{,.gz,.Z}/" "c/-/( f n s o od os h X nice b e dt w d sl szonly unsat)/"
@@ -37,35 +45,27 @@ complete g_rdf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr
 complete g_rms "n/-tu/( ps fs ns us ms s m h)/" "n/-what/( rmsd rho rhosc)/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-mir/f:*.xvg{,.gz,.Z}/" "n/-a/f:*.xvg{,.gz,.Z}/" "n/-dist/f:*.xvg{,.gz,.Z}/" "n/-m/f:*.xpm{,.gz,.Z}/" "n/-bin/f:*.dat{,.gz,.Z}/" "n/-bm/f:*.xpm{,.gz,.Z}/" "c/-/( s f f2 n o mir a dist m bin bm h X nice b e dt tu w what nopbc nofit prev split skip skip2 max min bmax bmin nlevels)/"
 complete g_rmsdist "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-equiv/f:*.dat{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-rms/f:*.xpm{,.gz,.Z}/" "n/-scl/f:*.xpm{,.gz,.Z}/" "n/-mean/f:*.xpm{,.gz,.Z}/" "n/-nmr3/f:*.xpm{,.gz,.Z}/" "n/-nmr6/f:*.xpm{,.gz,.Z}/" "n/-noe/f:*.dat{,.gz,.Z}/" "c/-/( f s n equiv o rms scl mean nmr3 nmr6 noe h X nice b e dt w nlevels max nosumh)/"
 complete g_rmsf "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-oq/f:*.pdb{,.gz,.Z}/" "n/-ox/f:*.pdb{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-dir/f:*.log{,.gz,.Z}/" "c/-/( f s n q oq ox o od oc dir h X nice b e dt w res aniso)/"
-complete g_rotacf "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
+complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-deshuf/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-pp/f:*.top{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-t/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14)/"
+complete g_rotacf "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit)/"
 complete g_saltbr "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h X nice b e dt t sep)/"
-complete g_sas "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-r/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-ao/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "c/-/( f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip noprot)/"
+complete g_sas "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-r/f:*.xvg{,.gz,.Z}/" "n/-q/f:*.pdb{,.gz,.Z}/" "n/-ao/f:*.xvg{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "c/-/( f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip nopbc noprot dgs)/"
 complete g_sgangle "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-od/f:*.xvg{,.gz,.Z}/" "n/-od1/f:*.xvg{,.gz,.Z}/" "n/-od2/f:*.xvg{,.gz,.Z}/" "c/-/( f n s oa od od1 od2 h X nice b e dt w)/"
 complete g_sorient "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-no/f:*.xvg{,.gz,.Z}/" "n/-ro/f:*.xvg{,.gz,.Z}/" "n/-co/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o no ro co h X nice b e dt w com rmin rmax nbin)/"
 complete g_tcaf "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-oa/f:*.xvg{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-oc/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ot oa o of oc ov h X nice b e dt w mol k34 wt)/"
-complete g_traj "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ox/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ob/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-ekr/f:*.xvg{,.gz,.Z}/" "c/-/( f s n ox ov of ob ot ekr h X nice b e dt tu w com mol nojump nox noy noz len)/"
-complete g_velacc "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac)/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
-complete genbox "n/-cp/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-cs/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-ci/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "c/-/( cp cs ci o p h X nice box nmol try seed vdwd shell)/"
-complete genconf "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-trj/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber)/"
-complete genion "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-pot/f:*.pdb{,.gz,.Z}/" "c/-/( s n o g pot h X nice np pname pq nn nname nq rmin random seed)/"
-complete genpr "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.itp{,.gz,.Z}/" "c/-/( f n o h X nice fc)/"
-complete gmxcheck "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-f2/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s1/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-s2/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-c/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-e2/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol)/"
-complete gmxdump "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "c/-/( s f e h X nice nonr)/"
-complete grompp "n/-f/f:*.mdp{,.gz,.Z}/" "n/-po/f:*.mdp{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-r/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-deshuf/f:*.ndx{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-pp/f:*.top{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-t/f:*.{trr,trj}{,.gz,.Z}/" "c/-/( f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14)/"
+complete g_traj "n/-tu/( ps fs ns us ms s m h)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-ox/f:*.xvg{,.gz,.Z}/" "n/-ov/f:*.xvg{,.gz,.Z}/" "n/-of/f:*.xvg{,.gz,.Z}/" "n/-ob/f:*.xvg{,.gz,.Z}/" "n/-ot/f:*.xvg{,.gz,.Z}/" "n/-ekt/f:*.xvg{,.gz,.Z}/" "n/-ekr/f:*.xvg{,.gz,.Z}/" "n/-cv/f:*.pdb{,.gz,.Z}/" "n/-cf/f:*.pdb{,.gz,.Z}/" "c/-/( f s n ox ov of ob ot ekt ekr cv cf h X nice b e dt tu w com mol nojump nox noy noz len)/"
+complete g_velacc "n/-P/( 0 1 2 3)/" "n/-fitfn/( none exp aexp exp_exp vac exp5 exp7)/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.xvg{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit)/"
 complete highway "n/-f/f:*.dat{,.gz,.Z}/" "n/-a/f:*.dat{,.gz,.Z}/" "c/-/( f a h X nice b e dt)/"
 complete make_ndx "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.ndx{,.gz,.Z}/" "c/-/( f n o h X nice)/"
-complete mdrun "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dgdl/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-eo/f:*.edo{,.gz,.Z}/" "n/-pi/f:*.ppa{,.gz,.Z}/" "n/-po/f:*.ppa{,.gz,.Z}/" "n/-pd/f:*.pdo{,.gz,.Z}/" "n/-pn/f:*.ndx{,.gz,.Z}/" "c/-/( s o x c e g dgdl table rerun ei eo pi po pd pn h X nice deffnm np v nocompact)/"
+complete mdrun "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dgdl/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-eo/f:*.edo{,.gz,.Z}/" "n/-j/f:*.gct{,.gz,.Z}/" "n/-jo/f:*.gct{,.gz,.Z}/" "n/-ffout/f:*.xvg{,.gz,.Z}/" "n/-devout/f:*.xvg{,.gz,.Z}/" "n/-runav/f:*.xvg{,.gz,.Z}/" "n/-pi/f:*.ppa{,.gz,.Z}/" "n/-po/f:*.ppa{,.gz,.Z}/" "n/-pd/f:*.pdo{,.gz,.Z}/" "n/-pn/f:*.ndx{,.gz,.Z}/" "n/-mtx/f:*.mtx{,.gz,.Z}/" "c/-/( s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn mtx h X nice deffnm np v nocompact multi glas ionize)/"
 complete mk_angndx "n/-type/( angle g96-angle dihedral improper ryckaert-bellemans phi-psi)/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( s n h X nice type)/"
 complete ngmx "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( f s n h X nice b e dt)/"
-complete nmrun "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-m/f:*.mtx{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "c/-/( s m g h X nice np v nocompact)/"
-complete pdb2gmx "n/-dummy/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "c/-/( f o p i n q h X nice merge inter ss ter lys asp glu his angle dist una nosort H14 ignh alldih dummy heavyh deuterate)/"
+complete pdb2gmx "n/-dummy/( none hydrogens aromatics)/" "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-p/f:*.top{,.gz,.Z}/" "n/-i/f:*.itp{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-q/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "c/-/( f o p i n q h X nice merge inter ss ter lys asp glu his angle dist posrefc una nosort H14 ignh alldih dummy heavyh deuterate)/"
 complete protonate "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( s f n o h X nice b e dt)/"
-complete tpbconv "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( s f n o h X nice time extend until nounconstrained)/"
-complete trjcat "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( o n h X nice b e dt prec novel settime nosort)/"
+complete tpbconv "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-f/f:*.{trr,trj}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( s f n o h X nice time extend until zeroq nounconstrained)/"
+complete trjcat "n/-tu/( ps fs ns us ms s m h)/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "c/-/( o n h X nice tu b e dt prec novel settime nosort cat)/"
 complete trjconv "n/-tu/( ps fs ns us ms s m h)/" "n/-pbc/( none whole inbox nojump)/" "n/-ur/( rect tric compact)/" "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-fr/f:*.ndx{,.gz,.Z}/" "c/-/( f o s n fr h X nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit pfit ndec novel force trunc exec app split sep)/"
 complete trjorder "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa,gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-n/f:*.ndx{,.gz,.Z}/" "n/-o/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "c/-/( f s n o h X nice b e dt na da)/"
 complete wheel "n/-f/f:*.dat{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "c/-/( f o h X nice r0 rot0 T nonn)/"
-complete x2top "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.top{,.gz,.Z}/" "n/-r/f:*.rtp{,.gz,.Z}/" "c/-/( f o r h X nice kb kt kp nexcl H14 alldih noround nopairs name)/"
-complete xmdrun "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.{trr,trj}{,.gz,.Z}/" "n/-x/f:*.xtc{,.gz,.Z}/" "n/-c/f:*.{gro,g96,pdb,brk,ent}{,.gz,.Z}/" "n/-e/f:*.{edr,ene}{,.gz,.Z}/" "n/-g/f:*.log{,.gz,.Z}/" "n/-dgdl/f:*.xvg{,.gz,.Z}/" "n/-table/f:*.xvg{,.gz,.Z}/" "n/-rerun/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-ei/f:*.edi{,.gz,.Z}/" "n/-eo/f:*.edo{,.gz,.Z}/" "n/-j/f:*.gct{,.gz,.Z}/" "n/-jo/f:*.gct{,.gz,.Z}/" "n/-ffout/f:*.xvg{,.gz,.Z}/" "n/-devout/f:*.xvg{,.gz,.Z}/" "n/-runav/f:*.xvg{,.gz,.Z}/" "n/-pi/f:*.ppa{,.gz,.Z}/" "n/-po/f:*.ppa{,.gz,.Z}/" "n/-pd/f:*.pdo{,.gz,.Z}/" "n/-pn/f:*.ndx{,.gz,.Z}/" "c/-/( s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn h X nice deffnm np v nocompact multi glas ionize)/"
+complete x2top "n/-f/f:*.{gro,g96,pdb,brk,ent,tpr,tpb,tpa}{,.gz,.Z}/" "n/-o/f:*.top{,.gz,.Z}/" "n/-r/f:*.rtp{,.gz,.Z}/" "c/-/( f o r h X nice scale nexcl H14 alldih nopairs name nopbc param noround kb kt kp)/"
 complete xpm2ps "n/-title/( top once ylabel none)/" "n/-legend/( both first second none)/" "n/-diag/( first second none)/" "n/-combine/( halves add sub mult div)/" "n/-rainbow/( no blue red)/" "n/-f/f:*.xpm{,.gz,.Z}/" "n/-f2/f:*.xpm{,.gz,.Z}/" "n/-di/f:*.m2p{,.gz,.Z}/" "n/-do/f:*.m2p{,.gz,.Z}/" "n/-o/f:*.eps{,.gz,.Z}/" "n/-xpm/f:*.xpm{,.gz,.Z}/" "c/-/( f f2 di do o xpm h X nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline)/"
 complete xrama "n/-f/f:*.{xtc,trr,trj,gro,g96,pdb,g87}{,.gz,.Z}/" "n/-s/f:*.{tpr,tpb,tpa}{,.gz,.Z}/" "c/-/( f s h X nice b e dt)/"

diff --git a/scripts/completion.zsh b/scripts/completion.zsh
index 82f50d6f17f475128292d34a9236f74f30256017..d2cce69ab47447207160d7eec6e8cbda0912e1ec 100644 (file)
--- a/scripts/completion.zsh
+++ b/scripts/completion.zsh
@@ -1,24 +1,30 @@
 compctl  -x 's[-]' -s " f s n ssdump map o sc a ta aa h X nice b e dt tu w sss" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ssdump]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-map]' -g '*.map(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-sc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ta]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-aa]' -g '*.xvg(|.gz|.Z) *(/)' -- do_dssp
 compctl  -x 's[-]' -s " f n o bf h X nice w ndef bt box angles d c center rotate princ scale density pbc mead grasp rvdw atom legend label" - 'c[-1,-bt]' -s " tric cubic dodecahedron octahedron" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-bf]' -g '*.dat(|.gz|.Z) *(/)' -- editconf
 compctl  -x 's[-]' -s " f o h X nice b e dt offset settime nosort scalefac noerror" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- eneconv
+compctl  -x 's[-]' -s " s g table parm ga h X nice tol fmax epot nocomb npow ratio logeps nov" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-parm]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-ga]' -g '*.dat(|.gz|.Z) *(/)' -- ffscan
 compctl  -x 's[-]' -s " v v2 f s n eig1 eig2 disp proj 2d 3d filt extr over inpr h X nice b e dt tu w first last skip max nframes split" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-v2]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-eig1]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-eig2]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-disp]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-proj]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-2d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-3d]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-filt]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-extr]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-over]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-inpr]' -g '*.xpm(|.gz|.Z) *(/)' -- g_anaeig
-compctl  -x 's[-]' -s " f ac msd cc dist av ee h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-errbar]' -s " none stddev error 90" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-msd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ee]' -g '*.xvg(|.gz|.Z) *(/)' -- g_analyze
-compctl  -x 's[-]' -s " f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-type]' -s " angle dihedral improper ryckaert-bellemans" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_angle
-compctl  -x 's[-]' -s " f n o l h X nice b e dt w blen tol noaver" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' -- g_bond
+compctl  -x 's[-]' -s " f ac msd cc dist av ee g h X nice w notime b e n d bw errbar power nosubav oneacf acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-errbar]' -s " none stddev error 90" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-msd]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ee]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_analyze
+compctl  -x 's[-]' -s " f s n od ov of ot oh oc h X nice b e dt w type all binwidth chandler avercorr acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-type]' -s " angle dihedral improper ryckaert-bellemans" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oh]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' -- g_angle
+compctl  -x 's[-]' -s " f n s o l d h X nice b e dt w blen tol noaver" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' -- g_bond
 compctl  -x 's[-]' -s " f s n ol od oz ot otr otl ok okr okl oa h X nice b e dt tu na z" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-otl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ok]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-okl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.pdb(|.gz|.Z) *(/)' -- g_bundle
-compctl  -x 's[-]' -s " c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-maxchi]' -s " 0 1 2 3 4 5 6" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ss]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-jc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_chi
-compctl  -x 's[-]' -s " f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff max skip av wcl nst rmsmin method binary M P seed niter kT" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ev]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tr]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ntr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-clid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cl]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
+compctl  -x 's[-]' -s " c f o p ss jc corr g h X nice b e dt w r0 phi psi omega rama viol all shift run maxchi nonormhisto ramomega bfact bmax acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-maxchi]' -s " 0 1 2 3 4 5 6" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ss]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-jc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- g_chi
+compctl  -x 's[-]' -s " f s n dm o g dist ev sz tr ntr clid cl h X nice b e dt tu w dista nlevels keepfree cutoff nofit max skip av wcl nst rmsmin method binary M P seed niter kT" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-method]' -s " linkage jarvis-patrick monte-carlo diagonalization gromos" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ev]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-sz]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-tr]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-ntr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-clid]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cl]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_cluster
+compctl  -x 's[-]' -s " f n o nc mc ac h X nice b e dt w cut nskip nlevels rgblo rgbhi" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' -- g_clustsize
 compctl  -x 's[-]' -s " f1 f2 o n1 n2 h X nice one pbc" - 'c[-1,-f1]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n1]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-n2]' -g '*.ndx(|.gz|.Z) *(/)' -- g_confrms
 compctl  -x 's[-]' -s " f s n o v av l xpm xpma h X nice b e dt tu nofit ref mwa last" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-av]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-xpma]' -g '*.xpm(|.gz|.Z) *(/)' -- g_covar
 compctl  -x 's[-]' -s " f n s ei o h X nice b e dt w d sl number ed count" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_density
-compctl  -x 's[-]' -s " f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-ffn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dielectric
+compctl  -x 's[-]' -s " f d o c h X nice b e dt w fft nox1 eint bfit efit tail A tau1 tau2 eps0 epsRF fix ffn nsmooth" - 'c[-1,-ffn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dielectric
 compctl  -x 's[-]' -s " f s o h X nice b e dt w sa mult" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' -- g_dih
-compctl  -x 's[-]' -s " enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-enx]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
+compctl  -x 's[-]' -s " enx f s n o e a d c g q h X nice b e dt w mu mumax epsilonRF skip temp avercorr gkratom acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-enx]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-d]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dipoles
 compctl  -x 's[-]' -s " s f ds da dn dm dr l n h X nice b e dt w ntop" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ds]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-da]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dn]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dm]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-l]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_disre
 compctl  -x 's[-]' -s " f s n o h X nice b e dt dist" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_dist
 compctl  -x 's[-]' -s " f o n h X nice firstangle lastangle nframe maxangle trans head tail" - 'c[-1,-f]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_dyndom
+compctl  -x 's[-]' -s " cp cs ci o p h X nice box nmol try seed vdwd shell" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
+compctl  -x 's[-]' -s " f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
 compctl  -x 's[-]' -s " f groups eref emat etot h X nice b e dt w sum skip nomean nlevels max min nocoul coulr coul14 nolj lj14 bham nofree temp" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-groups]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-eref]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-emat]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-etot]' -g '*.xvg(|.gz|.Z) *(/)' -- g_enemat
-compctl  -x 's[-]' -s " f f2 s o viol pairs corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pairs]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-vis]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ravg]' -g '*.xvg(|.gz|.Z) *(/)' -- g_energy
+compctl  -x 's[-]' -s " f f2 s o viol pairs ora ort oda odr odt corr vis ravg h X nice b e w fee fetemp zero sum dp mutot skip aver nmol ndf fluc orinst acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-viol]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pairs]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ora]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ort]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oda]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-odt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-corr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-vis]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ravg]' -g '*.xvg(|.gz|.Z) *(/)' -- g_energy
+compctl  -x 's[-]' -s " s n o g pot h X nice np pname pq nn nname nq rmin random seed" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' -- genion
+compctl  -x 's[-]' -s " f n o h X nice fc" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' -- genpr
 compctl  -x 's[-]' -s " f s o n h X nice b e dt w q p" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_gyrate
 compctl  -x 's[-]' -s " f n nm s o h X nice b e dt w d sl" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-nm]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_h2order
 compctl  -x 's[-]' -s " f s n g sel num ac dist ang hx hbn hbm da h X nice b e dt ins a r abin rbin nonitacc shell" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-sel]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-num]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ac]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ang]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hx]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-hbn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-hbm]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-da]' -g '*.xvg(|.gz|.Z) *(/)' -- g_hbond
@@ -28,6 +34,8 @@ compctl  -x 's[-]' -s " f s n mean frames no h X nice b e dt t nlevels" - 'c[-1,
 compctl  -x 's[-]' -s " f s n od on o h X nice b e dt w matrix d pi" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-on]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.out(|.gz|.Z) *(/)' -- g_mindist
 compctl  -x 's[-]' -s " f1 f2 o or n h X nice w ninterm first last nofit" - 'c[-1,-f1]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-or]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- g_morph
 compctl  -x 's[-]' -s " f s n o mol h X nice b e dt tu w type lateral ngroup nomw trestart beginfit endfit" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-type]' -s " no x y z" - 'c[-1,-lateral]' -s " no x y z" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mol]' -g '*.xvg(|.gz|.Z) *(/)' -- g_msd
+compctl  -x 's[-]' -s " f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol lastener" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s1]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-s2]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxcheck
+compctl  -x 's[-]' -s " s f e h X nice nonr" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxdump
 compctl  -x 's[-]' -s " f s o v h X nice nom first last" - 'c[-1,-f]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- g_nmeig
 compctl  -x 's[-]' -s " v e s n o h X nice temp seed num first last" - 'c[-1,-v]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- g_nmens
 compctl  -x 's[-]' -s " f n s o od os h X nice b e dt w d sl szonly unsat" - 'c[-1,-d]' -s " z x y" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-os]' -g '*.xvg(|.gz|.Z) *(/)' -- g_order
@@ -37,35 +45,27 @@ compctl  -x 's[-]' -s " f s n o sq cn hq image h X nice b e dt w bin com cut fad
 compctl  -x 's[-]' -s " s f f2 n o mir a dist m bin bm h X nice b e dt tu w what nopbc nofit prev split skip skip2 max min bmax bmin nlevels" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-what]' -s " rmsd rho rhosc" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-mir]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dist]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-bin]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-bm]' -g '*.xpm(|.gz|.Z) *(/)' -- g_rms
 compctl  -x 's[-]' -s " f s n equiv o rms scl mean nmr3 nmr6 noe h X nice b e dt w nlevels max nosumh" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-equiv]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rms]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-scl]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-mean]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr3]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-nmr6]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-noe]' -g '*.dat(|.gz|.Z) *(/)' -- g_rmsdist
 compctl  -x 's[-]' -s " f s n q oq ox o od oc dir h X nice b e dt w res aniso" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-oq]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-dir]' -g '*.log(|.gz|.Z) *(/)' -- g_rmsf
-compctl  -x 's[-]' -s " f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rotacf
+compctl  -x 's[-]' -s " f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-deshuf]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-pp]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-t]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- grompp
+compctl  -x 's[-]' -s " f s n o h X nice b e dt w d noaver acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_rotacf
 compctl  -x 's[-]' -s " f s h X nice b e dt t sep" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- g_saltbr
-compctl  -x 's[-]' -s " f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip noprot" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ao]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' -- g_sas
+compctl  -x 's[-]' -s " f s o r q ao n i h X nice b e dt w solsize ndots qmax minarea skip nopbc noprot dgs" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-ao]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' -- g_sas
 compctl  -x 's[-]' -s " f n s oa od od1 od2 h X nice b e dt w" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od1]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-od2]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sgangle
 compctl  -x 's[-]' -s " f s n o no ro co h X nice b e dt w com rmin rmax nbin" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-no]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ro]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-co]' -g '*.xvg(|.gz|.Z) *(/)' -- g_sorient
 compctl  -x 's[-]' -s " f s n ot oa o of oc ov h X nice b e dt w mol k34 wt" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oa]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-oc]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' -- g_tcaf
-compctl  -x 's[-]' -s " f s n ox ov of ob ot ekr h X nice b e dt tu w com mol nojump nox noy noz len" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ob]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekr]' -g '*.xvg(|.gz|.Z) *(/)' -- g_traj
-compctl  -x 's[-]' -s " f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_velacc
-compctl  -x 's[-]' -s " cp cs ci o p h X nice box nmol try seed vdwd shell" - 'c[-1,-cp]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-cs]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-ci]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' -- genbox
-compctl  -x 's[-]' -s " f o trj h X nice nbox dist seed rot shuffle sort block nmolat maxrot renumber" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-trj]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- genconf
-compctl  -x 's[-]' -s " s n o g pot h X nice np pname pq nn nname nq rmin random seed" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-pot]' -g '*.pdb(|.gz|.Z) *(/)' -- genion
-compctl  -x 's[-]' -s " f n o h X nice fc" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.itp(|.gz|.Z) *(/)' -- genpr
-compctl  -x 's[-]' -s " f f2 s1 s2 c e e2 h X nice vdwfac bonlo bonhi tol" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s1]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-s2]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-e2]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxcheck
-compctl  -x 's[-]' -s " s f e h X nice nonr" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' -- gmxdump
-compctl  -x 's[-]' -s " f po c r n deshuf p pp o t h X nice nov time np shuffle sort normdumbds load maxwarn check14" - 'c[-1,-f]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.mdp(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-deshuf]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-pp]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-t]' -g '*.(trr|trj)(|.gz|.Z) *(/)' -- grompp
+compctl  -x 's[-]' -s " f s n ox ov of ob ot ekt ekr cv cf h X nice b e dt tu w com mol nojump nox noy noz len" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-ox]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ov]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-of]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ob]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ot]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekt]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-ekr]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-cv]' -g '*.pdb(|.gz|.Z) *(/)' - 'c[-1,-cf]' -g '*.pdb(|.gz|.Z) *(/)' -- g_traj
+compctl  -x 's[-]' -s " f s n o h X nice b e dt w mol acflen nonormalize P fitfn ncskip beginfit endfit" - 'c[-1,-P]' -s " 0 1 2 3" - 'c[-1,-fitfn]' -s " none exp aexp exp_exp vac exp5 exp7" - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.xvg(|.gz|.Z) *(/)' -- g_velacc
 compctl  -x 's[-]' -s " f a h X nice b e dt" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-a]' -g '*.dat(|.gz|.Z) *(/)' -- highway
 compctl  -x 's[-]' -s " f n o h X nice" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.ndx(|.gz|.Z) *(/)' -- make_ndx
-compctl  -x 's[-]' -s " s o x c e g dgdl table rerun ei eo pi po pd pn h X nice deffnm np v nocompact" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dgdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-eo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-pi]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-pd]' -g '*.pdo(|.gz|.Z) *(/)' - 'c[-1,-pn]' -g '*.ndx(|.gz|.Z) *(/)' -- mdrun
+compctl  -x 's[-]' -s " s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn mtx h X nice deffnm np v nocompact multi glas ionize" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dgdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-eo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-j]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-jo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-ffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-devout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-runav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pi]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-pd]' -g '*.pdo(|.gz|.Z) *(/)' - 'c[-1,-pn]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-mtx]' -g '*.mtx(|.gz|.Z) *(/)' -- mdrun
 compctl  -x 's[-]' -s " s n h X nice type" - 'c[-1,-type]' -s " angle g96-angle dihedral improper ryckaert-bellemans phi-psi" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- mk_angndx
 compctl  -x 's[-]' -s " f s n h X nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- ngmx
-compctl  -x 's[-]' -s " s m g h X nice np v nocompact" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-m]' -g '*.mtx(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' -- nmrun
-compctl  -x 's[-]' -s " f o p i n q h X nice merge inter ss ter lys asp glu his angle dist una nosort H14 ignh alldih dummy heavyh deuterate" - 'c[-1,-dummy]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' -- pdb2gmx
+compctl  -x 's[-]' -s " f o p i n q h X nice merge inter ss ter lys asp glu his angle dist posrefc una nosort H14 ignh alldih dummy heavyh deuterate" - 'c[-1,-dummy]' -s " none hydrogens aromatics" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-p]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-i]' -g '*.itp(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-q]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' -- pdb2gmx
 compctl  -x 's[-]' -s " s f n o h X nice b e dt" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- protonate
-compctl  -x 's[-]' -s " s f n o h X nice time extend until nounconstrained" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- tpbconv
-compctl  -x 's[-]' -s " o n h X nice b e dt prec novel settime nosort" - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- trjcat
+compctl  -x 's[-]' -s " s f n o h X nice time extend until zeroq nounconstrained" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-f]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- tpbconv
+compctl  -x 's[-]' -s " o n h X nice tu b e dt prec novel settime nosort cat" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' -- trjcat
 compctl  -x 's[-]' -s " f o s n fr h X nice b e tu w skip dt dump t0 timestep pbc ur center box shift fit pfit ndec novel force trunc exec app split sep" - 'c[-1,-tu]' -s " ps fs ns us ms s m h" - 'c[-1,-pbc]' -s " none whole inbox nojump" - 'c[-1,-ur]' -s " rect tric compact" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-fr]' -g '*.ndx(|.gz|.Z) *(/)' -- trjconv
 compctl  -x 's[-]' -s " f s n o h X nice b e dt na da" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa|gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-n]' -g '*.ndx(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' -- trjorder
 compctl  -x 's[-]' -s " f o h X nice r0 rot0 T nonn" - 'c[-1,-f]' -g '*.dat(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' -- wheel
-compctl  -x 's[-]' -s " f o r h X nice kb kt kp nexcl H14 alldih noround nopairs name" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.rtp(|.gz|.Z) *(/)' -- x2top
-compctl  -x 's[-]' -s " s o x c e g dgdl table rerun ei eo j jo ffout devout runav pi po pd pn h X nice deffnm np v nocompact multi glas ionize" - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.(trr|trj)(|.gz|.Z) *(/)' - 'c[-1,-x]' -g '*.xtc(|.gz|.Z) *(/)' - 'c[-1,-c]' -g '*.(gro|g96|pdb|brk|ent)(|.gz|.Z) *(/)' - 'c[-1,-e]' -g '*.(edr|ene)(|.gz|.Z) *(/)' - 'c[-1,-g]' -g '*.log(|.gz|.Z) *(/)' - 'c[-1,-dgdl]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-table]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-rerun]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-ei]' -g '*.edi(|.gz|.Z) *(/)' - 'c[-1,-eo]' -g '*.edo(|.gz|.Z) *(/)' - 'c[-1,-j]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-jo]' -g '*.gct(|.gz|.Z) *(/)' - 'c[-1,-ffout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-devout]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-runav]' -g '*.xvg(|.gz|.Z) *(/)' - 'c[-1,-pi]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-po]' -g '*.ppa(|.gz|.Z) *(/)' - 'c[-1,-pd]' -g '*.pdo(|.gz|.Z) *(/)' - 'c[-1,-pn]' -g '*.ndx(|.gz|.Z) *(/)' -- xmdrun
+compctl  -x 's[-]' -s " f o r h X nice scale nexcl H14 alldih nopairs name nopbc param noround kb kt kp" - 'c[-1,-f]' -g '*.(gro|g96|pdb|brk|ent|tpr|tpb|tpa)(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.top(|.gz|.Z) *(/)' - 'c[-1,-r]' -g '*.rtp(|.gz|.Z) *(/)' -- x2top
 compctl  -x 's[-]' -s " f f2 di do o xpm h X nice w noframe title yonce legend diag combine bx by rainbow gradient skip zeroline" - 'c[-1,-title]' -s " top once ylabel none" - 'c[-1,-legend]' -s " both first second none" - 'c[-1,-diag]' -s " first second none" - 'c[-1,-combine]' -s " halves add sub mult div" - 'c[-1,-rainbow]' -s " no blue red" - 'c[-1,-f]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-f2]' -g '*.xpm(|.gz|.Z) *(/)' - 'c[-1,-di]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-do]' -g '*.m2p(|.gz|.Z) *(/)' - 'c[-1,-o]' -g '*.eps(|.gz|.Z) *(/)' - 'c[-1,-xpm]' -g '*.xpm(|.gz|.Z) *(/)' -- xpm2ps
 compctl  -x 's[-]' -s " f s h X nice b e dt" - 'c[-1,-f]' -g '*.(xtc|trr|trj|gro|g96|pdb|g87)(|.gz|.Z) *(/)' - 'c[-1,-s]' -g '*.(tpr|tpb|tpa)(|.gz|.Z) *(/)' -- xrama

diff --git a/share/html/online.html b/share/html/online.html
index 09215765c04d4c1e17a83502f101273f8949bb0e..79cfe473e6785bc0e66aafa88725f5c8b0149a12 100644 (file)
--- a/share/html/online.html
+++ b/share/html/online.html
@@ -20,7 +20,7 @@ Online Reference</h2>
 </TABLE></TD>
 <td ALIGN=RIGHT VALIGN=BOTTOM WIDTH="*" NOSAVE>
 <B>VERSION 3.1<br>
-Tue 15 May 2001</B></td>
+Wed 27 Feb 2002</B></td>
 </tr>
 </table>
 
@@ -49,6 +49,7 @@ Tue 15 May 2001</B></td>
 <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/ffscan.html>ffscan</a>
 <br><a href=online/g_anaeig.html>g_anaeig</a>
 <br><a href=online/g_analyze.html>g_analyze</a>
 <br><a href=online/g_angle.html>g_angle</a>
@@ -56,6 +57,7 @@ Tue 15 May 2001</B></td>
 <br><a href=online/g_bundle.html>g_bundle</a>
 <br><a href=online/g_chi.html>g_chi</a>
 <br><a href=online/g_cluster.html>g_cluster</a>
+<br><a href=online/g_clustsize.html>g_clustsize</a>
 <br><a href=online/g_confrms.html>g_confrms</a>
 <br><a href=online/g_covar.html>g_covar</a>
 <br><a href=online/g_density.html>g_density</a>
@@ -65,8 +67,12 @@ Tue 15 May 2001</B></td>
 <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>
@@ -76,6 +82,8 @@ Tue 15 May 2001</B></td>
 <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>
@@ -85,6 +93,7 @@ Tue 15 May 2001</B></td>
 <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>
@@ -93,19 +102,11 @@ Tue 15 May 2001</B></td>
 <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/make_ndx.html>make_ndx</a>
 <br><a href=online/mdrun.html>mdrun</a>
 <br><a href=online/mk_angndx.html>mk_angndx</a>
 <br><a href=online/ngmx.html>ngmx</a>
-<br><a href=online/nmrun.html>nmrun</a>
 <br><a href=online/pdb2gmx.html>pdb2gmx</a>
 <br><a href=online/protonate.html>protonate</a>
 <br><a href=online/tpbconv.html>tpbconv</a>
@@ -114,7 +115,6 @@ Tue 15 May 2001</B></td>
 <br><a href=online/trjorder.html>trjorder</a>
 <br><a href=online/wheel.html>wheel</a>
 <br><a href=online/x2top.html>x2top</a>
-<br><a href=online/xmdrun.html>xmdrun</a>
 <br><a href=online/xpm2ps.html>xpm2ps</a>
 <br><a href=online/xrama.html>xrama</a>
 </multicol>
@@ -224,6 +224,7 @@ Tue 15 May 2001</B></td>
 <TR><TD COLSPAN=2><b>Distances in structures over time</b>
 <TR><TD><A HREF="online/g_mindist.html">g_mindist</A></TD><TD>calculates the minimum distance between two groups</TD>
 <TR><TD><A HREF="online/g_dist.html">g_dist</A></TD><TD>calculates the distances between the centers of mass of two groups</TD>
+<TR><TD><A HREF="online/g_bond.html">g_bond</A></TD><TD>calculates distances between atoms</TD>
 <TR><TD><A HREF="online/g_mdmat.html">g_mdmat</A></TD><TD>calculates residue contact maps</TD>
 <TR><TD><A HREF="online/g_rmsdist.html">g_rmsdist</A></TD><TD>calculates atom pair distances averaged with power 2, -3 or -6</TD>
 </TABLE>
@@ -328,6 +329,5 @@ Tue 15 May 2001</B></td>
 <hr>
 <div ALIGN=RIGHT>
 <font size="-1"><a href="http://www.gromacs.org">http://www.gromacs.org</a></font><br>
-<font size="-1"><a href="mailto:gromacs@gromacs.org">gromacs@gromacs.org</a></font><br>
 </body>
 </html>

diff --git a/share/html/online/do_dssp.html b/share/html/online/do_dssp.html
index 47206ab4f8bc99d51e69944c6d26137d9f7c4df0..630779b58bfcfe83dc433077acf4b6b9b59e91d9 100644 (file)
--- a/share/html/online/do_dssp.html
+++ b/share/html/online/do_dssp.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>do_dssp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -18,11 +18,11 @@ do_dssp
 reads a trajectory file and computes the secondary structure for
 each time frame 
 calling the dssp program. If you do not have the dssp program,
-get it. do_dssp assumes that the dssp executable is in
-/home/mdgroup/dssp/dssp. If that is not the case, then you should
+get it. do_dssp assumes that the dssp executable is
+/usr/local/bin/dssp. If this is not the case, then you should
 set an environment variable <b>DSSP</b> pointing to the dssp
-executable as in: <p>
-<tt>setenv DSSP /usr/local/bin/dssp</tt><p>
+executable, e.g.: <p>
+<tt>setenv DSSP /opt/dssp/bin/dssp</tt><p>
 The structure assignment for each residue and time is written to an
 <tt>.<a href="xpm.html">xpm</a></tt> matrix file. This file can be visualized with for instance
 <tt>xv</tt> and can be converted to postscript with <tt><a href="xpm2ps.html">xpm2ps</a></tt>.
@@ -33,7 +33,7 @@ Solvent accessible surface (SAS) per residue can be calculated, both in
 absolute values (A^2) and in fractions of the maximal accessible
 surface of a residue. The maximal accessible surface is defined as
 the accessible surface of a residue in a chain of glycines.
-[B]Note[b] that the program <tt><a href="g_sas.html">g_sas</a></tt> can also compute SAS
+<b>Note</b> that the program <tt><a href="g_sas.html">g_sas</a></tt> can also compute SAS
 and that is more efficient.<p>
 Finally, this program can dump the secondary structure in a special file
 <tt>ssdump.<a href="dat.html">dat</a></tt> for usage in the program <tt><a href="g_chi.html">g_chi</a></tt>. Together

diff --git a/share/html/online/editconf.html b/share/html/online/editconf.html
index ee0e04f740f605f329b9f304f8d4a6c121f1d773..062da22f2362cd2388a8952272e0a68637c294fe 100644 (file)
--- a/share/html/online/editconf.html
+++ b/share/html/online/editconf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>editconf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>editconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -86,7 +86,7 @@ Finally with option <tt>-label</tt> editconf can add a chain identifier
 to a <a href="pdb.html">pdb</a> file, which can be useful for analysis with e.g. rasmol.<p>
 To convert a truncated octrahedron file produced by a package which uses
 a cubic box with the corners cut off (such as Gromos) use:<br>
-<tt>editconf -f &lt;infile&gt; -rotate 0 -45 -35.2644 -bt o -box &lt;veclen&gt; -o &lt;outfile&gt;</tt><br>
+<tt>editconf -f &lt;in&gt; -rotate 0 -45 -35.264 -bt o -box &lt;veclen&gt; -o &lt;out&gt;</tt><br>
 where <tt>veclen</tt> is the size of the cubic box times sqrt(3)/2.
 <P>
 <H3>Files</H3>

diff --git a/share/html/online/eneconv.html b/share/html/online/eneconv.html
index c82192af2218eb3300247ce660941f2d03cc7174..46adec01a6ff73362fbcbee0fc4c02a7f65170f4 100644 (file)
--- a/share/html/online/eneconv.html
+++ b/share/html/online/eneconv.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>eneconv</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>eneconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_anaeig.html b/share/html/online/g_anaeig.html
index 782bfabc62b92f031d91ec55a67f5fe108b89228..0c5af7505b2897ecda800670acfa3099d2d81ac4 100644 (file)
--- a/share/html/online/g_anaeig.html
+++ b/share/html/online/g_anaeig.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_anaeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_analyze.html b/share/html/online/g_analyze.html
index e93309af85fac83ffb5a6502bd9c7b61de2cf147..371f9d9791a07c5d85ba662cadc8611ed10dc3b1 100644 (file)
--- a/share/html/online/g_analyze.html
+++ b/share/html/online/g_analyze.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_analyze</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_analyze</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -72,6 +72,7 @@ zero or negative value are ignored.
 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   distr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-av</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> average.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ee</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  errest.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-g</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">  fitlog.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
 </TABLE>
 <P>
 <H3>Other options</H3>
@@ -94,7 +95,7 @@ zero or negative value are ignored.
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_angle.html b/share/html/online/g_angle.html
index 60135d17ebb171db42b9924e958e1a133cd51849..8a7d92a794db4e6e009dbfcd654f0e9bb96ce64f 100644 (file)
--- a/share/html/online/g_angle.html
+++ b/share/html/online/g_angle.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_angle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -59,7 +59,7 @@ If this is not the case, the program will crash.
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_bond.html b/share/html/online/g_bond.html
index 0c2d5028dacb595787f9a31e2f6105bbfbd4cb2d..4c80d39d2444a4f7381d9dde6ef3e675fe561b3a 100644 (file)
--- a/share/html/online/g_bond.html
+++ b/share/html/online/g_bond.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bond</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -20,15 +20,20 @@ bonds are read from a single group in the index file in order i1-j1
 i2-j2 thru in-jn.<p>
 <tt>-tol</tt> gives the half-width of the distribution as a fraction
 of the bondlength (<tt>-blen</tt>). That means, for a bond of 0.2
-a tol of 0.1 gives a distribution from 0.18 to 0.22
+a tol of 0.1 gives a distribution from 0.18 to 0.22.<p>
+Option <tt>-d</tt> plots all the distances as a function of time.
+This requires a structure file for the atom and residue names in
+the output.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input, Opt. </TD><TD> Structure+mass(db): <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   bonds.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-l</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="log.html">   bonds.log</a></tt> </TD><TD> Output, Opt. </TD><TD> Log file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-d</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">distance.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 </TABLE>
 <P>
 <H3>Other options</H3>

diff --git a/share/html/online/g_bundle.html b/share/html/online/g_bundle.html
index 61e12855d520ddf52b349a56fac03e6d7715f5dc..4e9fc74c4ba2b6ba2a4714a84d5d87512806d817 100644 (file)
--- a/share/html/online/g_bundle.html
+++ b/share/html/online/g_bundle.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_bundle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_chi.html b/share/html/online/g_chi.html
index 3ebbec7abe33eed931f9558c90a29399ae9ba517..894642dfc1da28c5600ce85ceabd0013382a5d17 100644 (file)
--- a/share/html/online/g_chi.html
+++ b/share/html/online/g_chi.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_chi</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_chi</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -72,7 +72,7 @@ the average omega angle is plotted using color coding.
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_cluster.html b/share/html/online/g_cluster.html
index 78d02b686a8fd0f6e00f7c44cf328e3a416af266..16eabcf8626e46d5a9b389bf32d2fa09b8ba0a02 100644 (file)
--- a/share/html/online/g_cluster.html
+++ b/share/html/online/g_cluster.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_cluster</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -93,6 +93,7 @@ for a selected set of clusters (with option <tt>-wcl</tt>, depends on
 <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>-keepfree</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>-4</tt> </TD><TD> if &gt;0 # levels not to use when coloring clusters; if &lt;0 nlevels/-keepfree+1 levels will not be used </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-cutoff</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.1</tt> </TD><TD> RMSD cut-off (nm) for two structures to be neighbor </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]fit</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Use least squares fitting before RMSD calculation </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-max</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> Maximum level in RMSD matrix </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Only analyze every nr-th frame </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]av</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Write average iso middle structure for each cluster </TD></TD>

diff --git a/share/html/online/g_confrms.html b/share/html/online/g_confrms.html
index 131000438ca36e55adc5f8d7b553c2dc14356398..6c91e0f865f496a72a8d0861b7cea5cb6ef63d0e 100644 (file)
--- a/share/html/online/g_confrms.html
+++ b/share/html/online/g_confrms.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_confrms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_covar.html b/share/html/online/g_covar.html
index 819e4919e8e5a8e4585d074ee2056d88545d10c3..bd4f72c7ccdd39892a4941f1469fa5a72991fb41 100644 (file)
--- a/share/html/online/g_covar.html
+++ b/share/html/online/g_covar.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_covar</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_density.html b/share/html/online/g_density.html
index 771a841e4a1bc971f51bf04c3056543b57db7c1d..436169e954b8281d49242f91fb4a1cb3157c29c0 100644 (file)
--- a/share/html/online/g_density.html
+++ b/share/html/online/g_density.html
@@ -4,19 +4,27 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_density</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_density</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</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
+in kg/m^3, number densities or electron densities can be
+calculated. For electron densities, a file describing the number of
+electrons for each type of atom should be provided using <tt>-ei</tt>.
+It should look like:<br>
+   2<br>
+   atomname = nrelectrons<br>
+   atomname = nrelectrons<br>
+The first line contains the number of lines to read from the file.
+There should be one line for each unique atom name in your system.
+The number of electrons for each atom is modified by its atomic
 partial charge.
 <P>
 <H3>Files</H3>
@@ -25,7 +33,7 @@ partial charge.
 <TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    traj.xtc</a></tt> </TD><TD> Input </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-n</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">   index.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-s</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   topol.tpr</a></tt> </TD><TD> Input </TD><TD> Generic run input: <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">electrons.dat</a></tt> </TD><TD> Output </TD><TD> Generic data file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="dat.html">electrons.dat</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic data file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> density.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
 </TABLE>
 <P>

diff --git a/share/html/online/g_dielectric.html b/share/html/online/g_dielectric.html
index f99f59c6b29d429634515cb0a4b548047dc01021..a6e73c3766cd3b95e7ba66d8b52339fe86107bc6 100644 (file)
--- a/share/html/online/g_dielectric.html
+++ b/share/html/online/g_dielectric.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dielectric</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -68,7 +68,7 @@ plot should be one half of a circle
 <TR><TD ALIGN=RIGHT> <b><tt>-eps0</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>    80</tt> </TD><TD> Epsilon 0 of your liquid </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-epsRF</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>  78.5</tt> </TD><TD> Epsilon of the reaction field used in your simulation. A value of 0 means infinity. </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-fix</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>0</tt> </TD><TD> Fix parameters at their start values, A (2), tau1 (1), or tau2 (4) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt> or <tt>vac</tt> </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-ffn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_dih.html b/share/html/online/g_dih.html
index 4012bac3ec731f52aec1669c8b3ae0b5386c9ea6..63d604e065ce89aa7f50a1c1a1d53664fc0c5d3d 100644 (file)
--- a/share/html/online/g_dih.html
+++ b/share/html/online/g_dih.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dih</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_dipoles.html b/share/html/online/g_dipoles.html
index 710440a4afd3d84683c89d6bd2ceb8971c0cbdca..2fd846f3c3113171bf894b6bed6847b12046fd1c 100644 (file)
--- a/share/html/online/g_dipoles.html
+++ b/share/html/online/g_dipoles.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dipoles</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -33,7 +33,9 @@ a rectangular or cubic simulation box is used.<p>
 Option <tt>-g</tt> produces a plot of the distance dependent Kirkwood
 G-factor, as well as the average cosine of the angle between the dipoles
 as a function of the distance. The plot also includes gOO and hOO
-according to Nymand & Linse, JCP 112 (2000) pp 6386-6395.<p>
+according to Nymand & Linse, JCP 112 (2000) pp 6386-6395. In the same plot
+we also include the energy per scale computed by taking the inner product of
+the dipoles divided by the distance to the third power.<p>
 <p>
 EXAMPLES<p>
 g_dipoles -P1 -n mols -o dip_sqr -mu 2.273 -mumax 5.0
@@ -82,7 +84,7 @@ distribution function a maximum of 5.0 will be used.
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_disre.html b/share/html/online/g_disre.html
index 3ed003effbc6ed8dcba01402dd89912450b57584..cd393ea9342c9ea598ba4505651287b6dd77acb5 100644 (file)
--- a/share/html/online/g_disre.html
+++ b/share/html/online/g_disre.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_disre</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_dist.html b/share/html/online/g_dist.html
index e8f2913911f7c2c507e19a69d59ca8f2103c70c2..49171633a485b238994bfce7af5d26246759c2d0 100644 (file)
--- a/share/html/online/g_dist.html
+++ b/share/html/online/g_dist.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dist</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -18,7 +18,9 @@ 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>
 Or when <tt>-dist</tt> is set, print all the atoms in group 2 that are
-closer than a certain distance to the center of mass of group 1.
+closer than a certain distance to the center of mass of group 1.<p>
+Other programs that calculate distances are <tt><a href="g_mindist.html">g_mindist</a></tt>
+and <tt><a href="g_bond.html">g_bond</a></tt>.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>

diff --git a/share/html/online/g_dyndom.html b/share/html/online/g_dyndom.html
index d197fcbbcce3a01afcf8d3e765163b4505369dcd..8464e5edba0178cec47c21b0a30fb1fb96fe0277 100644 (file)
--- a/share/html/online/g_dyndom.html
+++ b/share/html/online/g_dyndom.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_dyndom</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_enemat.html b/share/html/online/g_enemat.html
index db1260ca425591efa3ce1acc99924ff713931fb8..39e3d1d04f8a4f33deea8cdb33c217bfaa416694 100644 (file)
--- a/share/html/online/g_enemat.html
+++ b/share/html/online/g_enemat.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_enemat</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_enemat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_energy.html b/share/html/online/g_energy.html
index 4834d97c1b58fc0f61111d04b9ae5fc874ccf467..6aedbc04906aba7a207474d20bc0215974358329 100644 (file)
--- a/share/html/online/g_energy.html
+++ b/share/html/online/g_energy.html
@@ -4,28 +4,41 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_energy</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</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>
+Average and RMSD are calculated with full precision from the
+simulation (see printed manual). Drift is calculated by performing
+a LSQ fit of the data to a straight line. Total drift is drift
+multiplied by total time.<p>
 When the <tt>-viol</tt> option is set, the time averaged
 violations are plotted and the running time-averaged and
 instantaneous sum of violations are recalculated. Additionally
 running time-averaged and instantaneous distances between
 selected pairs can be plotted with the <tt>-pairs</tt> option.<p>
-Average and RMSD are calculated with full precision from the
-simulation (see printed manual). Drift is calculated by performing
-a LSQ fit of the data to a straight line. Total drift is drift
-multiplied by total time.<p>
+Options <tt>-ora</tt>, <tt>-ort</tt>, <tt>-oda</tt>, <tt>-odr</tt> and
+<tt>-odt</tt> are used for analyzing orientation restraint data.
+The first two options plot the orientation, the last three the
+deviations of the orientations from the experimental values.
+The options that end on an 'a' plot the average over time
+as a function of restraint. The options that end on a 't'
+prompt the user for restraint label numbers and plot the data
+as a function of time. Option <tt>-odr</tt> plots the RMS
+deviation as a function of restraint.
+When the run used time or ensemble averaged orientation restraints,
+option <tt>-orinst</tt> can be used to analyse the instantaneous,
+not ensemble-averaged orientations and deviations instead of
+the time and ensemble averages.<p>
 With <tt>-fee</tt> a free energy estimate is calculated using
 the formula: G = -ln &lt; e ^ (E/kT) &gt; * kT, where k is Boltzmann's
 constant, T is set by <tt>-fetemp</tt> and the average is over the
@@ -49,6 +62,11 @@ the energies must both be calculated from the same trajectory.
 <TR><TD ALIGN=RIGHT> <b><tt>-o</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">  energy.xvg</a></tt> </TD><TD> Output </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-viol</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">violaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-pairs</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   pairs.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ora</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orienta.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ort</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orientt.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-oda</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> orideva.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-odr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-odt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> oridevt.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-corr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> enecorr.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-vis</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   visco.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ravg</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">runavgdf.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
@@ -74,10 +92,11 @@ the energies must both be calculated from the same trajectory.
 <TR><TD ALIGN=RIGHT> <b><tt>-nmol</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Number of molecules in your sample: the energies are divided by this number </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-ndf</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of degrees of freedom per molecule. Necessary for calculating the heat capacity </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]fluc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Calculate autocorrelation of energy fluctuations rather than energy itself </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]orinst</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Analyse instantaneous orientation data </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_gyrate.html b/share/html/online/g_gyrate.html
index 3552c1c7f4b8204ec0b1ad8657ed487bc1f49d54..b4a0c2883da2693bd3edf86d64d42042bb201d72 100644 (file)
--- a/share/html/online/g_gyrate.html
+++ b/share/html/online/g_gyrate.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_gyrate</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_gyrate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_h2order.html b/share/html/online/g_h2order.html
index 9b9017d1fe0b70eaad5dfd532ed7d4a878177445..a2d4c2c21e088d9acffaab442a1b00e0a2ff1907 100644 (file)
--- a/share/html/online/g_h2order.html
+++ b/share/html/online/g_h2order.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_h2order</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_h2order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_hbond.html b/share/html/online/g_hbond.html
index c605c952db9596aa5bb71d20b3a4f3d7f7970318..b3ca46b741f671997dcd07a761884ac74e72a737 100644 (file)
--- a/share/html/online/g_hbond.html
+++ b/share/html/online/g_hbond.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_hbond</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_helix.html b/share/html/online/g_helix.html
index 183ccc9db9965cbdaf21fe1ac7b3c09c334c7a10..a2135371fd5c7849e2e56796b13e718aaf796566 100644 (file)
--- a/share/html/online/g_helix.html
+++ b/share/html/online/g_helix.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helix</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_helix</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_lie.html b/share/html/online/g_lie.html
index 6f85346f80ea1af889bdd633cca66ce6abb773c1..7b0e80f4e4ef9085a57b0c7719583e17b77c012c 100644 (file)
--- a/share/html/online/g_lie.html
+++ b/share/html/online/g_lie.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_lie</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_mdmat.html b/share/html/online/g_mdmat.html
index 811a7e0426b22cb54efb7c62b48f88214da3aea2..372206c2ab2999a17952b9b8f4073ebe0725602a 100644 (file)
--- a/share/html/online/g_mdmat.html
+++ b/share/html/online/g_mdmat.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mdmat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_mindist.html b/share/html/online/g_mindist.html
index 472d712428aa8432e185ef25fe0325bed35833ff..6a11b6ca99ee2efcca93d137848ea559d32816e6 100644 (file)
--- a/share/html/online/g_mindist.html
+++ b/share/html/online/g_mindist.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_mindist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -23,8 +23,9 @@ periodic image is plotted. This is useful for checking if a protein
 has seen its periodic image during a simulation. Only one shift in
 each direction is considered, giving a total of 26 shifts.
 It also plots the maximum distance within the group and the lengths
-of the three box vectors.
-This option is very slow.
+of the three box vectors. This option is very slow.<p>
+Other programs that calculate distances are <tt><a href="g_dist.html">g_dist</a></tt>
+and <tt><a href="g_bond.html">g_bond</a></tt>.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>

diff --git a/share/html/online/g_morph.html b/share/html/online/g_morph.html
index 25a1d842e749eb937697fe83575db8fea97eaaf2..836a7080851650d5d2fb77d791cd9e075d50e772 100644 (file)
--- a/share/html/online/g_morph.html
+++ b/share/html/online/g_morph.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_morph</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_msd.html b/share/html/online/g_msd.html
index 456d81e13a2c562fe380ebb2efb8614359ba3bbf..9eb90f988dd267077178b77dfe7f68888cc8184e 100644 (file)
--- a/share/html/online/g_msd.html
+++ b/share/html/online/g_msd.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_msd</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_msd</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_nmeig.html b/share/html/online/g_nmeig.html
index 47ffc6ca0c0577e0e127bae536dfe1735e4967ec..86c8b6e5f2db0d42aaf513c807f60458b42827a6 100644 (file)
--- a/share/html/online/g_nmeig.html
+++ b/share/html/online/g_nmeig.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmeig</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_nmens.html b/share/html/online/g_nmens.html
index f6f1d95f898eb810c555ec3639ae1cfdb45b2b9d..5b027cea6a62dc9922f59fbda4a733faa85eb55a 100644 (file)
--- a/share/html/online/g_nmens.html
+++ b/share/html/online/g_nmens.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmens</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_nmens</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_order.html b/share/html/online/g_order.html
index 77cffde4483e36f25ff05825527cfbf5ff85d5ad..621153fd1fc76f5e014e85b701cb8378b96139c4 100644 (file)
--- a/share/html/online/g_order.html
+++ b/share/html/online/g_order.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_order</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_potential.html b/share/html/online/g_potential.html
index 6d8e39f1ff5b29102f65d7726012f79a725c9f27..e65ff23d7ce4111770c97bae63d15c76ca9fed47 100644 (file)
--- a/share/html/online/g_potential.html
+++ b/share/html/online/g_potential.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_potential</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_potential</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rama.html b/share/html/online/g_rama.html
index da78501883bc014158d88fb72a19909cdf9dd101..fbad15453c6ae28cee2ea0408a3001101b80e1b8 100644 (file)
--- a/share/html/online/g_rama.html
+++ b/share/html/online/g_rama.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rama</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rdf.html b/share/html/online/g_rdf.html
index 8af74358b65c3c1f2efb48c07479a33eb8ab3ca5..0f7dc04c40c615e1a7b5d7496c56423e9a1f5012 100644 (file)
--- a/share/html/online/g_rdf.html
+++ b/share/html/online/g_rdf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rdf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rms.html b/share/html/online/g_rms.html
index 9a891db0fed04d57771508ded9ee78134d5b99c4..2e7b326984a2b872f19d34d00f6c787b6c09cdfb 100644 (file)
--- a/share/html/online/g_rms.html
+++ b/share/html/online/g_rms.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rms</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rmsdist.html b/share/html/online/g_rmsdist.html
index a08231834d62d11cc67ae88b699733062de9e10f..9f67be7f9f2cb767b15dfbfe4394d2800a9dc10d 100644 (file)
--- a/share/html/online/g_rmsdist.html
+++ b/share/html/online/g_rmsdist.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsdist</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rmsf.html b/share/html/online/g_rmsf.html
index 6221b047917cbb6b01788df5c961b1fc66dc8968..2015f71c189df8f101e960698e9ad7733690b89d 100644 (file)
--- a/share/html/online/g_rmsf.html
+++ b/share/html/online/g_rmsf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rmsf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_rotacf.html b/share/html/online/g_rotacf.html
index bc5cc697425b701ea00dcb9e6e5e723357cd8015..114a901fd33e888f53697c64f335d296ac7f51b7 100644 (file)
--- a/share/html/online/g_rotacf.html
+++ b/share/html/online/g_rotacf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotacf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_rotacf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -57,7 +57,7 @@ to a two parameter exponential
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/g_saltbr.html b/share/html/online/g_saltbr.html
index 31a14c83e5624236004ba3471f88a9ce4d48a7d3..442045389a089f8d84cc48ceb43881d49a2562e2 100644 (file)
--- a/share/html/online/g_saltbr.html
+++ b/share/html/online/g_saltbr.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_saltbr</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_saltbr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_sas.html b/share/html/online/g_sas.html
index 277e0c0def29ca77c1b23f605b966756051c3d8a..48be6df17902048021acc64354cb465487e6141c 100644 (file)
--- a/share/html/online/g_sas.html
+++ b/share/html/online/g_sas.html
@@ -4,23 +4,25 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sas</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
-g_sas computes hydrophobic and total solvent accessible surface area.
+g_sas computes hydrophobic, hydrophilic 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
 connecting the nearest nodes as CONECT records. The area can be plotted
 per atom and per residue as well (option -ao). In combination with
 the latter option an <tt><a href="itp.html">itp</a></tt> file can be generated (option -i)
-which can be used to restrain surface atoms.
+which can be used to restrain surface atoms.<p>
+By default, periodic boundary conditions are taken into account,
+this can be turned off using the -pbc option.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -48,9 +50,11 @@ which can be used to restrain surface atoms.
 <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>
 <TR><TD ALIGN=RIGHT> <b><tt>-qmax</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.2</tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.5</tt> </TD><TD> The maximum charge (e, absolute value) of a hydrophobic atom </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-minarea</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.5</tt> </TD><TD> The minimum area (nm^2) to count an atom as a surface atom when writing a position restraint file  (see help) </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-skip</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>1</tt> </TD><TD> Do only every nth frame </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Take periodicity into account </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]prot</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Output the protein to the connelly <a href="pdb.html">pdb</a> file too </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dgs</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> default value for solvation free energy per area (kJ/mol/nm^2) </TD></TD>
 </TABLE>
 <P>
 <hr>

diff --git a/share/html/online/g_sgangle.html b/share/html/online/g_sgangle.html
index d3b3973b5f95bb191e7229ab675e5bc97d360c26..683ef21ac5eb557e5ad6f1f62c40a8a956700c95 100644 (file)
--- a/share/html/online/g_sgangle.html
+++ b/share/html/online/g_sgangle.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sgangle</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_sorient.html b/share/html/online/g_sorient.html
index 3a43d4352e2872b1f633ed0d50a3f4da3618fd70..1de81828340145da53f28832ab69256f2849ed5d 100644 (file)
--- a/share/html/online/g_sorient.html
+++ b/share/html/online/g_sorient.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_sorient</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_tcaf.html b/share/html/online/g_tcaf.html
index 6dda6be6b5a69eb39bfff0b98556c9586e0668d5..711e76cfa6cebc02906cbc34d809187f6f63eceb 100644 (file)
--- a/share/html/online/g_tcaf.html
+++ b/share/html/online/g_tcaf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_tcaf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/g_traj.html b/share/html/online/g_traj.html
index 28652a7ef277c1fc5f5b27903381ee8fcaf29c54..9798b7d11b22913bc2653750d75d2d99cdead056 100644 (file)
--- a/share/html/online/g_traj.html
+++ b/share/html/online/g_traj.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_traj</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_traj</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -21,10 +21,20 @@ 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,
-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>.
+No corrections are made for constrained degrees of freedom!
+This implies <tt>-com</tt>.<p>
+Options <tt>-ekt</tt> and <tt>-ekr</tt> plot the translational and
+rotational kinetic energy of each group,
+provided velocities are present in the trajectory file.
+This implies <tt>-com</tt>.<p>
+Options <tt>-cv</tt> and <tt>-cf</tt> write the average velocities
+and average forces as temperature factors to a <a href="pdb.html">pdb</a> file with
+the average coordinates. The temperature factors are scaled such
+that the maximum is 10. To get the velocities or forces of one
+frame set both <tt>-b</tt> and <tt>-e</tt> to the time of
+desired frame. When averaging over frames you might need to use
+the <tt>-nojump</tt> option to obtain the correct average coordinates.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -37,7 +47,10 @@ This implies <tt>-com</tt>.
 <TR><TD ALIGN=RIGHT> <b><tt>-of</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   force.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ob</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     box.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ot</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">    temp.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ekt</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> ektrans.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ekr</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">   ekrot.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cv</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   veloc.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-cf</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdb.html">   force.pdb</a></tt> </TD><TD> Output, Opt. </TD><TD> Protein data bank file </TD></TR>
 </TABLE>
 <P>
 <H3>Other options</H3>

diff --git a/share/html/online/g_velacc.html b/share/html/online/g_velacc.html
index d9d4891d58c5e2b874766c2594a0ce27551406c0..d80d948e7a4cfe7d6c50356e20d3e38278dbf4cc 100644 (file)
--- a/share/html/online/g_velacc.html
+++ b/share/html/online/g_velacc.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_velacc</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>g_velacc</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -44,7 +44,7 @@ of molecule numbers instead of atom numbers.
 <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): <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>-fitfn</tt></b> </TD><TD ALIGN=RIGHT> enum </TD><TD ALIGN=RIGHT> <tt>none</tt> </TD><TD> Fit function: <tt>none</tt>, <tt>exp</tt>, <tt>aexp</tt>, <tt>exp_exp</tt>, <tt>vac</tt>, <tt>exp5</tt> or <tt>exp7</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>

diff --git a/share/html/online/genbox.html b/share/html/online/genbox.html
index 99021ba9e89114fb83872353ca7cf43c28eef0a1..5f1f784932b630c1f09bfc25f77a90c16ea29b01 100644 (file)
--- a/share/html/online/genbox.html
+++ b/share/html/online/genbox.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genbox</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -38,8 +38,8 @@ solvent molecules. When no appropriately
 sized holes (holes that can hold an extra molecule) are available the 
 program tries for <tt>-nmol</tt> * <tt>-try</tt> times before giving up. 
 Increase -try if you have several small holes to fill.<p>
-The default solvent is Simple Point Charge water (SPC). The coordinates 
-for this are read from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. Other
+The default solvent is Simple Point Charge water (SPC), with coordinates 
+from <tt>$GMXLIB/spc216.<a href="gro.html">gro</a></tt>. Other
 solvents are also supported, as well as mixed solvents. The
 only restriction to solvent types is that a solvent molecule consists
 of exactly one residue. The residue information in the coordinate

diff --git a/share/html/online/genconf.html b/share/html/online/genconf.html
index d050818345fcb192ab03d76c3bdf3c9a9a8d115b..be471350a8994da430dbc23a2dcefaea9e0bc6d3 100644 (file)
--- a/share/html/online/genconf.html
+++ b/share/html/online/genconf.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genconf</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/genion.html b/share/html/online/genion.html
index 35763801f7bc0a3e9be6303d34ab39d76ff5eff4..71992b83f489abc43f200cdb919c504199df5919 100644 (file)
--- a/share/html/online/genion.html
+++ b/share/html/online/genion.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genion</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/genpr.html b/share/html/online/genpr.html
index 79f301bb31f13bd5b642a274d67a036426911210..864c36bfc1e56d92cbdd65847e0db67528062d2a 100644 (file)
--- a/share/html/online/genpr.html
+++ b/share/html/online/genpr.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genpr</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>genpr</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/gmxcheck.html b/share/html/online/gmxcheck.html
index 03c410baf09525a2c628aec3680aaa3136d9d553..da391275060f655eb729eb8e07e0ea194a936841 100644 (file)
--- a/share/html/online/gmxcheck.html
+++ b/share/html/online/gmxcheck.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxcheck</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxcheck</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -49,7 +49,8 @@ when both <tt>-s1</tt> and <tt>-s2</tt> are supplied.
 <TR><TD ALIGN=RIGHT> <b><tt>-vdwfac</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.8</tt> </TD><TD> Fraction of sum of VdW radii used as warning cutoff </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-bonlo</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.4</tt> </TD><TD> Min. fract. of sum of VdW radii for bonded atoms </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-bonhi</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.7</tt> </TD><TD> Max. fract. of sum of VdW radii for bonded atoms </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Tolerance for comparing real values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-tol</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Relative tolerance for comparing real values defined as 2*(a-b)/(|a|+|b|) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-lastener</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure. </TD></TD>
 </TABLE>
 <P>
 <hr>

diff --git a/share/html/online/gmxdump.html b/share/html/online/gmxdump.html
index 19a8b22afbc14b5a4fa0cba7da98bbce9545db9b..2be9264cc205d32a306f629a920a7e33b4caf9e2 100644 (file)
--- a/share/html/online/gmxdump.html
+++ b/share/html/online/gmxdump.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>gmxdump</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/grompp.html b/share/html/online/grompp.html
index b20d328f2cd4426703179f97eed3450acc176c59..aa6ec05298ea19504663a82ed5ea0fe4c442613f 100644 (file)
--- a/share/html/online/grompp.html
+++ b/share/html/online/grompp.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>grompp</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -31,6 +31,11 @@ NEMD parameters, which are corrected so that the net acceleration
 is zero.
 Eventually a binary file is produced that can serve as the sole input
 file for the MD program.<p>
+grompp uses the atom names from the topology file. The atom names
+in the coordinate file (option <tt>-c</tt>) are only read to generate
+warnings when they do not match the atom names in the topology.
+Note that the atom names are irrelevant for the simulation as
+only the atom types are used for generating interaction parameters.<p>
 grompp calls the c-preprocessor to resolve includes, macros 
 etcetera. To specify a macro-preprocessor other than /lib/cpp 
 (such as m4)
@@ -85,7 +90,7 @@ program.
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
 <TR><TH>option</TH><TH>filename</TH><TH>type</TH><TH>description</TH></TR>
-<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">  grompp.mdp</a></tt> </TD><TD> Input </TD><TD> grompp input file with MD parameters </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-f</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">  grompp.mdp</a></tt> </TD><TD> Input, Opt. </TD><TD> grompp input file with MD parameters </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mdp.html">   mdout.mdp</a></tt> </TD><TD> Output </TD><TD> grompp input file with MD parameters </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-c</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-r</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">    conf.gro</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic structure: <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> <a href="tpr.html">tpr</a> <a href="tpb.html">tpb</a> <a href="tpa.html">tpa</a> </TD></TR>

diff --git a/share/html/online/highway.html b/share/html/online/highway.html
index 867faab3519d324d9dccbf377a30038b644ea1ff..fc86c240816ede0d412b2fe356546f01e23d1f27 100644 (file)
--- a/share/html/online/highway.html
+++ b/share/html/online/highway.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>highway</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>highway</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/make_ndx.html b/share/html/online/make_ndx.html
index 6615c163801ff6331f67ad8cb768e9198aaae8d8..91b1d47080a3650f5b2bb38dd4e534d11daf9bc5 100644 (file)
--- a/share/html/online/make_ndx.html
+++ b/share/html/online/make_ndx.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>make_ndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/mdrun.html b/share/html/online/mdrun.html
index db814bb44d12818ada161d2ab78c1a076e39eb87..3913954df161226c536f30b231dedfe0da0bce3b 100644 (file)
--- a/share/html/online/mdrun.html
+++ b/share/html/online/mdrun.html
@@ -4,18 +4,25 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdrun</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mdrun</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</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
+The mdrun program is the main computational chemistry engine
+within GROMACS. Obviously, it performs Molecular Dynamics simulations,
+but it can also perform Brownian Dynamics and Langevin Dynamics
+as well as Conjugate Gradient or Steepest Descents energy minimization.
+Normal mode analysis is another option. In this case mdrun
+builds a Hessian matrix from single conformation.
+For usual Normal Modes-like calculations, make sure that
+the structure provided is properly energy-minimised.
+The generated matrix can be diagonalized by <a href="g_nmeig.html">g_nmeig</a>.<p>The mdrun program reads the run input file (<tt>-s</tt>) and distributes the
 topology over nodes if needed. The coordinates are passed
 around, so that computations can begin.
 First a neighborlist is made, then the forces are computed.
@@ -65,6 +72,11 @@ In both cases all the usual output will be written to file.
 When running with MPI, a signal to one of the mdrun processes
 is sufficient, this signal should not be sent to mpirun or
 the mdrun process that is the parent of the others.
+Finally some experimental algorithms can be tested when the
+appropriate options have been given. Currently under
+investigation are: polarizibility, glass simulations, 
+Free energy perturbation, X-Ray bombardments
+and parallel independent simulations.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -80,10 +92,16 @@ the mdrun process that is the parent of the others.
 <TR><TD ALIGN=RIGHT> <b><tt>-rerun</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="files.html">   rerun.xtc</a></tt> </TD><TD> Input, Opt. </TD><TD> Generic trajectory: <a href="xtc.html">xtc</a> <a href="trr.html">trr</a> <a href="trj.html">trj</a> <a href="gro.html">gro</a> <a href="g96.html">g96</a> <a href="pdb.html">pdb</a> </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-ei</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edi.html">     sam.edi</a></tt> </TD><TD> Input, Opt. </TD><TD> ED sampling input </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-eo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="edo.html">     sam.edo</a></tt> </TD><TD> Output, Opt. </TD><TD> ED sampling output </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-j</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">    wham.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-jo</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="gct.html">     bam.gct</a></tt> </TD><TD> Input, Opt. </TD><TD> General coupling stuff </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-ffout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">     gct.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-devout</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html">deviatie.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-runav</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="xvg.html"> runaver.xvg</a></tt> </TD><TD> Output, Opt. </TD><TD> xvgr/xmgr file </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-pi</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html">    pull.ppa</a></tt> </TD><TD> Input, Opt. </TD><TD> Pull parameters </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-po</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ppa.html"> pullout.ppa</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull parameters </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-pd</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="pdo.html">    pull.pdo</a></tt> </TD><TD> Output, Opt. </TD><TD> Pull data output </TD></TR>
 <TR><TD ALIGN=RIGHT> <b><tt>-pn</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="ndx.html">    pull.ndx</a></tt> </TD><TD> Input, Opt. </TD><TD> Index file </TD></TR>
+<TR><TD ALIGN=RIGHT> <b><tt>-mtx</tt></b> </TD><TD ALIGN=RIGHT> <tt><a href="mtx.html">      nm.mtx</a></tt> </TD><TD> Output, Opt. </TD><TD> Hessian matrix </TD></TR>
 </TABLE>
 <P>
 <H3>Other options</H3>
@@ -96,6 +114,9 @@ the mdrun process that is the parent of the others.
 <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 &gt; 1) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]glas</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Do glass simulation with special long range corrections </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]ionize</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Do a simulation including the effect of an X-Ray bombardment on your system </TD></TD>
 </TABLE>
 <P>
 <hr>

diff --git a/share/html/online/mk_angndx.html b/share/html/online/mk_angndx.html
index 23a8f306035791c39910e45fb2641e2ea4f48de5..1b2a8cb3d74ccf1784915c0d497d0ee20de8587d 100644 (file)
--- a/share/html/online/mk_angndx.html
+++ b/share/html/online/mk_angndx.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mk_angndx</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>mk_angndx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/ngmx.html b/share/html/online/ngmx.html
index 4fe2028df17b90ba79242019e61864d58ab7be38..7c327f24be4f73bcce9129c3ab32e8a9612f4f1b 100644 (file)
--- a/share/html/online/ngmx.html
+++ b/share/html/online/ngmx.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>ngmx</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>ngmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/pdb2gmx.html b/share/html/online/pdb2gmx.html
index ec03a9bd5f9c3f098ea4b108a797983b84a9526a..5857f8a9c676f45121880e93d0f21b3f6761c519 100644 (file)
--- a/share/html/online/pdb2gmx.html
+++ b/share/html/online/pdb2gmx.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>pdb2gmx</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -105,6 +105,7 @@ Reference Feenstra et al., J. Comput. Chem. 20, 786 (1999).
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]his</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Interactive Histidine selection, iso checking H-bonds </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-angle</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   135</tt> </TD><TD> Minimum hydrogen-donor-acceptor angle for a H-bond (degrees) </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-dist</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   0.3</tt> </TD><TD> Maximum donor-acceptor distance for a H-bond (nm) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-posrefc</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>  1000</tt> </TD><TD> Force constant for position restraints </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]una</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Select aromatic rings with united CH atoms on Phenylalanine, Tryptophane and Tyrosine </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Sort the residues according to database </TD></TD>
 <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>

diff --git a/share/html/online/protonate.html b/share/html/online/protonate.html
index 64d4a13d2032d621dc258165e2b6a147742ffd7a..705dd812dce49b677a9029bde0612cbd99bcdd4a 100644 (file)
--- a/share/html/online/protonate.html
+++ b/share/html/online/protonate.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>protonate</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>protonate</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/tpbconv.html b/share/html/online/tpbconv.html
index 5bf145568df0d38bd3d8580b2b944115ab0fec86..d18ad09c0b422f83d79859731ae16cb0f1d61a3c 100644 (file)
--- a/share/html/online/tpbconv.html
+++ b/share/html/online/tpbconv.html
@@ -4,17 +4,17 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>tpbconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</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
+tpbconv can edit run input files in three 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.
 Note that a frame with coordinates and velocities is needed,
@@ -24,6 +24,9 @@ tpbconv and you have to start the run again from the beginning.<p>
 tpx file, which is useful when you want to remove the solvent from
 your tpx file, or when you want to make e.g. a pure Ca tpx file.
 <b>WARNING: this tpx file is not fully functional</b>.
+<b>3rd.</b> by setting the charges of a specified group
+to zero. This is useful when doing free energy estimates
+using the LIE (Linear Interactio Energy) method.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -43,6 +46,7 @@ your tpx file, or when you want to make e.g. a pure Ca tpx file.
 <TR><TD ALIGN=RIGHT> <b><tt>-time</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> Continue from frame at this time (ps) instead of the last frame </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-extend</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Extend runtime by this amount (ps) </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-until</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Extend runtime until this ending time (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]zeroq</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Set the charges of a group (from the index) to zero </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]unconstrained</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> For a continuous trajectory, the constraints should not be solved before the first step (default) </TD></TD>
 </TABLE>
 <P>

diff --git a/share/html/online/trjcat.html b/share/html/online/trjcat.html
index b7589252046098364109a530edb9cc6037ebba35..98f71da47cccbcfefe55960d8c39efba5351387d 100644 (file)
--- a/share/html/online/trjcat.html
+++ b/share/html/online/trjcat.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjcat</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjcat</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -19,7 +19,8 @@ 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 
 of each file. The input files are taken from the command line, 
 such that a command like <tt>trjcat -o fixed.<a href="trr.html">trr</a> *.<a href="trr.html">trr</a></tt> should do 
-the trick.
+the trick. Using <tt>-cat</tt> you can simply paste several files 
+together without removal of frames with identical time stamps.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -34,13 +35,15 @@ the trick.
 <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> real </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> First time to use </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> Last time to use </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Only write frame when t MOD dt = first time </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>-b</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> First time to use (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-e</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>    -1</tt> </TD><TD> Last time to use (ps) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-dt</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Only write frame when t MOD dt = first time (ps) </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-prec</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Precision for .<a href="xtc.html">xtc</a> and .<a href="gro.html">gro</a> writing in number of decimal places </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]vel</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Read and write velocities if possible </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]settime</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Change starting time interactively </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]sort</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Sort trajectory files (not frames) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]cat</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> do not discard double time frames </TD></TD>
 </TABLE>
 <P>
 <hr>

diff --git a/share/html/online/trjconv.html b/share/html/online/trjconv.html
index a284a513695bc5b652fd0f6a503c2e4b1e432ff0..2817e7ba568862fadd0a64640cddfa78104dd03c 100644 (file)
--- a/share/html/online/trjconv.html
+++ b/share/html/online/trjconv.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjconv</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjconv</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -43,7 +43,9 @@ Note that velocities are only supported in
 Option <tt>-app</tt> can be used to
 append output to an existing trajectory file.
 No checks are performed to ensure integrity
-of the resulting combined trajectory file.
+of the resulting combined trajectory file.<p>
+Option <tt>-sep</tt> can be used to write every frame to a seperate
+.<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file, default all frames all written to one file.
 <tt>.<a href="pdb.html">pdb</a></tt> files with all frames concatenated can be viewed with
 <tt>rasmol -nmrpdb</tt>.<p>
 It is possible to select part of your trajectory and write it out
@@ -140,7 +142,7 @@ one specific time from your trajectory.
 <TR><TD ALIGN=RIGHT> <b><tt>-exec</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt></tt> </TD><TD> Execute command for every output frame with the frame number as argument </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]app</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Append output </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-split</tt></b> </TD><TD ALIGN=RIGHT> time </TD><TD ALIGN=RIGHT> <tt>     0</tt> </TD><TD> Start writing new file when t MOD split = first time (ps) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]sep</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Write each frame to a separate .<a href="gro.html">gro</a>, .<a href="g96.html">g96</a> or .<a href="pdb.html">pdb</a> file </TD></TD>
 </TABLE>
 <P>
 <hr>

diff --git a/share/html/online/trjorder.html b/share/html/online/trjorder.html
index 82501f261c9f14bec4195dab8707879a93fda9d9..0e44f4a800bff92298f72cc0e5357b6157f4e5ae 100644 (file)
--- a/share/html/online/trjorder.html
+++ b/share/html/online/trjorder.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjorder</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>trjorder</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/wheel.html b/share/html/online/wheel.html
index 531e594db99fbc6baa6767de88cf7ea7765787a6..cf00a4788d1867ede48b7831ee42a12f5192a350 100644 (file)
--- a/share/html/online/wheel.html
+++ b/share/html/online/wheel.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>wheel</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>wheel</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/x2top.html b/share/html/online/x2top.html
index 130273978a3baa24eeaf24b3a9fd7d924273fe26..8680d71d6a3d4518a1b2af15d1e20017dea9e377 100644 (file)
--- a/share/html/online/x2top.html
+++ b/share/html/online/x2top.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>x2top</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>x2top</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>
@@ -18,7 +18,12 @@ 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.
 The program can also make an <a href="rtp.html">rtp</a> entry, which you can then add
-to the <a href="rtp.html">rtp</a> database.
+to the <a href="rtp.html">rtp</a> database.<p>
+When <tt>-param</tt> is set, equilibrium distances and angles
+and force constants will be printed in the topology for all
+interactions. The equilibrium distances and angles are taken
+from the input coordinates, the force constant are set with
+command line options.
 <P>
 <H3>Files</H3>
 <TABLE BORDER=1 CELLSPACING=0 CELLPADDING=2>
@@ -34,15 +39,18 @@ to the <a href="rtp.html">rtp</a> database.
 <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>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   400</tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     5</tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-scale</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   1.1</tt> </TD><TD> Scaling factor for bonds with unknown atom types relative to atom type O </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-nexcl</tt></b> </TD><TD ALIGN=RIGHT> int </TD><TD ALIGN=RIGHT> <tt>3</tt> </TD><TD> Number of exclusions </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]H14</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Use 3rd neighbour interactions for hydrogen atoms </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]alldih</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Generate all proper dihedrals </TD></TD>
-<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Round off measured values </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-[no]pairs</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Output 1-4 interactions (pairs) in topology file </TD></TD>
 <TR><TD ALIGN=RIGHT> <b><tt>-name</tt></b> </TD><TD ALIGN=RIGHT> string </TD><TD ALIGN=RIGHT> <tt>ICE</tt> </TD><TD> Name of your molecule </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]pbc</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Use periodic boundary conditions. Please set the GMXFULLPBC environment variable as well. </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]param</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>    no</tt> </TD><TD> Print parameters in the output </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-[no]round</tt></b> </TD><TD ALIGN=RIGHT> bool </TD><TD ALIGN=RIGHT> <tt>   yes</tt> </TD><TD> Round off measured values </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kb</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>400000</tt> </TD><TD> Bonded force constant (kJ/mol/nm^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kt</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>   400</tt> </TD><TD> Angle force constant (kJ/mol/rad^2) </TD></TD>
+<TR><TD ALIGN=RIGHT> <b><tt>-kp</tt></b> </TD><TD ALIGN=RIGHT> real </TD><TD ALIGN=RIGHT> <tt>     5</tt> </TD><TD> Dihedral angle force constant (kJ/mol/rad^2) </TD></TD>
 </TABLE>
 <P>
 <UL>

diff --git a/share/html/online/xpm2ps.html b/share/html/online/xpm2ps.html
index 2f953bd4628ec2c86a204186268cda0b93ec3191..90c4bbf8c7127e83d40d6320b586389ebaa8da39 100644 (file)
--- a/share/html/online/xpm2ps.html
+++ b/share/html/online/xpm2ps.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xpm2ps</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xpm2ps</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/share/html/online/xrama.html b/share/html/online/xrama.html
index 1029d607b4e7bacc18bc5c302e7a8d14344e0496..3935542923e6d8a5a7297c61b4a417f2aa291ffa 100644 (file)
--- a/share/html/online/xrama.html
+++ b/share/html/online/xrama.html
@@ -4,13 +4,13 @@
 <LINK rel=stylesheet href="style.css" type="text/css">
 <BODY text="#000000" bgcolor="#FFFFFF" link="#0000FF" vlink="#990000" alink="#FF0000">
 <TABLE WIDTH="98%" NOBORDER >
-<TR><TD WIDTH=300>
-<TABLE WIDTH=300 NOBORDER>
+<TR><TD WIDTH=400>
+<TABLE WIDTH=400 NOBORDER>
 <TD WIDTH=116>
 <a href="http://www.gromacs.org/"><img SRC="../images/gmxlogo_small.jpg"BORDER=0 height=133 width=116></a></td>
-<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xrama</h2><br><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
-</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.0<br>
-Tue 24 Jul 2001</B></td></tr></TABLE>
+<td ALIGN=LEFT VALIGN=TOP WIDTH=280><br><h2>xrama</h2><font size=-1><A HREF="../online.html">Main Table of Contents</A></font><br><br></td>
+</TABLE></TD><TD WIDTH="*" ALIGN=RIGHT VALIGN=BOTTOM><p><B>VERSION 3.1.beta_20020215<br>
+Wed 27 Feb 2002</B></td></tr></TABLE>
 <HR>
 <H3>Description</H3>
 <p>

diff --git a/src/gmxlib/disre.c b/src/gmxlib/disre.c
index 84abc16f025a6fd885ce593edddea6e36a69fd38..f17f2a2fe599b074ef8ba91d3e57dc5a76f247bc 100644 (file)
--- a/src/gmxlib/disre.c
+++ b/src/gmxlib/disre.c
@@ -172,7 +172,7 @@ void calc_disres_R_6(t_commrec *mcr,
     res++;
   }
   
-  if (mcr)
+  if ((mcr) && PAR(mcr))
     gmx_sum(2*dd->nr,Rt_6,mcr);
 }
 

diff --git a/src/gmxlib/main.c b/src/gmxlib/main.c
index fb488c0e39551e26cf863a8de37bf5acf6ead79f..3fe42cc7b68d6c37e8e9fd85fbc9d08f100b2e4b 100644 (file)
--- a/src/gmxlib/main.c
+++ b/src/gmxlib/main.c
@@ -146,7 +146,8 @@ void check_multi_int(FILE *log,t_commrec *mcr,int val,char *name)
   
   snew(ibuf,mcr->nnodes);
   ibuf[mcr->nodeid] = val;
-  gmx_sumi(mcr->nnodes,ibuf,mcr);
+  if((mcr) && PAR(mcr))
+    gmx_sumi(mcr->nnodes,ibuf,mcr);
   
   bCompatible = TRUE;
   for(p=1; p<mcr->nnodes; p++)
@@ -223,7 +224,9 @@ static void comm_args(t_commrec *cr,int *argc,char ***argv)
   
   if (!MASTER(cr))
     *argc=0;
-  gmx_sumi(1,argc,cr);
+
+  if((cr) && PAR(cr))
+    gmx_sumi(1,argc,cr);
   
   if (!MASTER(cr))
     snew(argv_tmp,*argc+1);

diff --git a/src/mdlib/Makefile.am b/src/mdlib/Makefile.am
index c864657c9a42a201ac63d349ab331a11cc3c6859..eeeed76cca6e1014742dd5b2ca17bddfb01ba1ea 100644 (file)
--- a/src/mdlib/Makefile.am
+++ b/src/mdlib/Makefile.am
@@ -23,7 +23,8 @@ libmd@LIBSUFFIX@_la_SOURCES = \
        psspread.c      shakef.c        sim_util.c      \
        splittop.c      tables.c        tgroup.c        \
        update.c        vcm.c           wnblist.c       \
-       poisson.h       splittop.h      wnblist.h
+       poisson.h       splittop.h      wnblist.h       \
+       pull-internal.h
 
 EXTRA_libmd@LIBSUFFIX@_la_SOURCES = \
        csettle.c       clincs.c        \

diff --git a/src/mdlib/tgroup.c b/src/mdlib/tgroup.c
index 9d505a8bbe249850c9dd98f23f9ee0c5a02f31a2..26189eb4878a97018aa11e673213e320158d6969 100644 (file)
--- a/src/mdlib/tgroup.c
+++ b/src/mdlib/tgroup.c
@@ -168,8 +168,9 @@ static void accumulate_ekin(t_commrec *cr,t_grpopts *opts,t_groups *grps)
 {
   int g;
 
-  for(g=0; (g<opts->ngtc); g++) 
-    gmx_sum(DIM*DIM,grps->tcstat[g].ekin[0],cr);
+  if(PAR(cr))
+    for(g=0; (g<opts->ngtc); g++) 
+      gmx_sum(DIM*DIM,grps->tcstat[g].ekin[0],cr);
 }       
 
 void update_grps(int start,int homenr,t_groups *grps,

diff --git a/src/mdlib/vcm.c b/src/mdlib/vcm.c
index a0d0ce2726a51fc8e62055cce61c6cd3891fb88a..933a8bcbcb60392e552db2ff351be158e4b29e91 100644 (file)
--- a/src/mdlib/vcm.c
+++ b/src/mdlib/vcm.c
@@ -79,7 +79,8 @@ t_vcm *init_vcm(FILE *fp,t_topology *top,t_commrec *cr,t_mdatoms *md,
     snew(mass,vcm->nr);
     for(g=0; (g<vcm->nr); g++)
       mass[g] = vcm->group_mass[g];
-    gmx_sum(vcm->nr,mass,cr);
+    if(PAR(cr))
+      gmx_sum(vcm->nr,mass,cr);
 
     /* Copy pointer to group names and print it. */
     fprintf(fp,"Center of mass motion removal mode is %s\n",ECOM(vcm->mode));