-## Process this file with automake to produce Makefile.in
-#
-# Don't edit - this file is generated automatically from Makefile.am
-#
+# This file has been generated by mknroff.pl. Don't edit it.
+man_MANS = \
+ anadock.1 \
+ do_dssp.1 \
+ editconf.1 \
+ eneconv.1 \
+ g_anaeig.1 \
+ g_analyze.1 \
+ g_angle.1 \
+ g_bond.1 \
+ g_bundle.1 \
+ g_chi.1 \
+ g_cluster.1 \
+ g_clustsize.1 \
+ g_confrms.1 \
+ g_covar.1 \
+ g_current.1 \
+ g_density.1 \
+ g_densmap.1 \
+ g_dielectric.1 \
+ g_dih.1 \
+ g_dipoles.1 \
+ g_disre.1 \
+ g_dist.1 \
+ g_dyndom.1 \
+ g_enemat.1 \
+ g_energy.1 \
+ g_filter.1 \
+ g_gyrate.1 \
+ g_h2order.1 \
+ g_hbond.1 \
+ g_helix.1 \
+ g_helixorient.1 \
+ g_kinetics.1 \
+ g_lie.1 \
+ g_mdmat.1 \
+ g_mindist.1 \
+ g_morph.1 \
+ g_msd.1 \
+ g_nmeig.1 \
+ g_nmens.1 \
+ g_nmtraj.1 \
+ g_order.1 \
+ g_polystat.1 \
+ g_potential.1 \
+ g_principal.1 \
+ g_rama.1 \
+ g_rdf.1 \
+ g_rms.1 \
+ g_rmsdist.1 \
+ g_rmsf.1 \
+ g_rotacf.1 \
+ g_saltbr.1 \
+ g_sas.1 \
+ g_sdf.1 \
+ g_sgangle.1 \
+ g_sham.1 \
+ g_sorient.1 \
+ g_spatial.1 \
+ g_spol.1 \
+ g_tcaf.1 \
+ g_traj.1 \
+ g_vanhove.1 \
+ g_velacc.1 \
+ g_wham.1 \
+ genbox.1 \
+ genconf.1 \
+ genion.1 \
+ genrestr.1 \
+ gmxcheck.1 \
+ gmxdump.1 \
+ grompp.1 \
+ highway.1 \
+ make_edi.1 \
+ make_ndx.1 \
+ mdrun.1 \
+ mk_angndx.1 \
+ ngmx.1 \
+ pdb2gmx.1 \
+ protonate.1 \
+ sigeps.1 \
+ tpbconv.1 \
+ trjcat.1 \
+ trjconv.1 \
+ trjorder.1 \
+ wheel.1 \
+ x2top.1 \
+ xpm2ps.1 \
+ xrama.1
-man_MANS = \
- anadock.1 g_cluster.1 g_filter.1 g_potential.1 \
- g_velacc.1 ngmx.1 g_clustsize.1 g_vanhove.1 \
- g_gyrate.1 g_rama.1 g_wham.1 pdb2gmx.1 \
- g_confrms.1 g_h2order.1 g_rdf.1 genrestr.1 \
- genbox.1 protonate.1 do_dssp.1 g_covar.1 \
- g_hbond.1 g_rms.1 genconf.1 tpbconv.1 \
- editconf.1 g_density.1 g_helix.1 g_rmsdist.1 \
- genion.1 trjcat.1 eneconv.1 g_dielectric.1 \
- g_lie.1 g_rmsf.1 trjconv.1 g_helixorient.1 \
- g_dih.1 g_mdmat.1 g_rotacf.1 sigeps.1 \
- gmxcheck.1 trjorder.1 g_anaeig.1 g_dipoles.1 \
- g_mindist.1 g_saltbr.1 gmxdump.1 wheel.1 \
- g_analyze.1 g_disre.1 g_morph.1 g_sas.1 \
- grompp.1 x2top.1 g_angle.1 g_dist.1 \
- g_msd.1 g_sgangle.1 highway.1 xpm2ps.1 \
- g_bond.1 g_dyndom.1 g_nmeig.1 g_sorient.1 \
- make_ndx.1 xrama.1 g_bundle.1 g_enemat.1 \
- g_nmens.1 g_tcaf.1 mdrun.1 g_chi.1 \
- g_energy.1 g_order.1 g_traj.1 mk_angndx.1 \
- g_densmap.1 g_sham.1 make_edi.1 g_spol.1 \
- g_spatial.1 g_sdf.1 g_rama.1 g_principal.1 \
- g_polystat.1 g_nmtraj.1 g_current.1
+EXTRA_DIST = ${man_MANS}
-EXTRA_DIST = ${man_MANS}
\ No newline at end of file
-.TH anadock 1 "Mon 22 Sep 2008"
+.TH anadock 1 "Thu 16 Oct 2008"
.SH NAME
-anadock
-.B VERSION 4.0_rc1
+anadock - cluster structures from Autodock runs
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3anadock\fP
.BI "-f" " eiwit.pdb "
-.TH do_dssp 1 "Mon 22 Sep 2008"
+.TH do_dssp 1 "Thu 16 Oct 2008"
.SH NAME
-do_dssp
-.B VERSION 4.0_rc1
+do_dssp - assigns secondary structure and calculates solvent accessible surface area
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3do_dssp\fP
.BI "-f" " traj.xtc "
-.TH editconf 1 "Mon 22 Sep 2008"
+.TH editconf 1 "Thu 16 Oct 2008"
.SH NAME
-editconf
-.B VERSION 4.0_rc1
+editconf - edits the box and writes subgroups
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3editconf\fP
.BI "-f" " conf.gro "
.BI "-[no]princ" ""
.BI "-scale" " vector "
.BI "-density" " real "
-.BI "-[no]vol" ""
.BI "-[no]pbc" ""
.BI "-[no]grasp" ""
.BI "-rvdw" " real "
Scaling is applied before any of the other operations are
-performed. Boxes can be scaled to give a certain density (option
+performed. Boxes and coordinates can be scaled to give a certain density (option
.B -density
-). A special feature of the scaling option, when the
+). Note that this may be inaccurate in case a gro
+file is given as input. A special feature of the scaling option, when the
factor -1 is given in one dimension, one obtains a mirror image,
mirrored in one of the plains, when one uses -1 in three dimensions
a point-mirror image is obtained.
.BI "-density" " real" " 1000 "
Density (g/l) of the output box achieved by scaling
-.BI "-[no]vol" "yes "
- Compute and print volume of the box
-
.BI "-[no]pbc" "no "
Remove the periodicity (make molecule whole again)
-.TH eneconv 1 "Mon 22 Sep 2008"
+.TH eneconv 1 "Thu 16 Oct 2008"
.SH NAME
-eneconv
-.B VERSION 4.0_rc1
+eneconv - converts energy files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3eneconv\fP
.BI "-f" " ener.edr "
-.TH g_anaeig 1 "Mon 22 Sep 2008"
+.TH g_anaeig 1 "Thu 16 Oct 2008"
.SH NAME
-g_anaeig
-.B VERSION 4.0_rc1
+g_anaeig - analyzes the eigenvectors
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_anaeig\fP
.BI "-v" " eigenvec.trr "
-.TH g_analyze 1 "Mon 22 Sep 2008"
+.TH g_analyze 1 "Thu 16 Oct 2008"
.SH NAME
-g_analyze
-.B VERSION 4.0_rc1
+g_analyze - analyzes data sets
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_analyze\fP
.BI "-f" " graph.xvg "
-.TH g_angle 1 "Mon 22 Sep 2008"
+.TH g_angle 1 "Thu 16 Oct 2008"
.SH NAME
-g_angle
-.B VERSION 4.0_rc1
+g_angle - calculates distributions and correlations for angles and dihedrals
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_angle\fP
.BI "-f" " traj.xtc "
-.TH g_bond 1 "Mon 22 Sep 2008"
+.TH g_bond 1 "Thu 16 Oct 2008"
.SH NAME
-g_bond
-.B VERSION 4.0_rc1
+g_bond - calculates distances between atoms
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_bond\fP
.BI "-f" " traj.xtc "
-.TH g_bundle 1 "Mon 22 Sep 2008"
+.TH g_bundle 1 "Thu 16 Oct 2008"
.SH NAME
-g_bundle
-.B VERSION 4.0_rc1
+g_bundle - analyzes bundles of axes, e.g. helices
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_bundle\fP
.BI "-f" " traj.xtc "
-.TH g_chi 1 "Mon 22 Sep 2008"
+.TH g_chi 1 "Thu 16 Oct 2008"
.SH NAME
-g_chi
-.B VERSION 4.0_rc1
+g_chi - calculates everything you want to know about chi and other dihedrals
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_chi\fP
.BI "-s" " conf.gro "
-.TH g_cluster 1 "Mon 22 Sep 2008"
+.TH g_cluster 1 "Thu 16 Oct 2008"
.SH NAME
-g_cluster
-.B VERSION 4.0_rc1
+g_cluster - clusters structures
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_cluster\fP
.BI "-f" " traj.xtc "
-.TH g_clustsize 1 "Mon 22 Sep 2008"
+.TH g_clustsize 1 "Thu 16 Oct 2008"
.SH NAME
-g_clustsize
-.B VERSION 4.0_rc1
+g_clustsize - calculate size distributions of atomic clusters
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_clustsize\fP
.BI "-f" " traj.xtc "
-.TH g_confrms 1 "Mon 22 Sep 2008"
+.TH g_confrms 1 "Thu 16 Oct 2008"
.SH NAME
-g_confrms
-.B VERSION 4.0_rc1
+g_confrms - fits two structures and calculates the rmsd
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_confrms\fP
.BI "-f1" " conf1.gro "
-.TH g_covar 1 "Mon 22 Sep 2008"
+.TH g_covar 1 "Thu 16 Oct 2008"
.SH NAME
-g_covar
-.B VERSION 4.0_rc1
+g_covar - calculates and diagonalizes the covariance matrix
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_covar\fP
.BI "-f" " traj.xtc "
-.TH g_current 1 "Mon 22 Sep 2008"
+.TH g_current 1 "Thu 16 Oct 2008"
.SH NAME
-g_current
-.B VERSION 4.0_rc1
+g_current - calculates dielectric constants for charged systems
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_current\fP
.BI "-s" " topol.tpr "
-.TH g_density 1 "Mon 22 Sep 2008"
+.TH g_density 1 "Thu 16 Oct 2008"
.SH NAME
-g_density
-.B VERSION 4.0_rc1
+g_density - calculates the density of the system
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_density\fP
.BI "-f" " traj.xtc "
-.TH g_densmap 1 "Mon 22 Sep 2008"
+.TH g_densmap 1 "Thu 16 Oct 2008"
.SH NAME
-g_densmap
-.B VERSION 4.0_rc1
+g_densmap - calculates 2D planar or axial-radial density maps
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_densmap\fP
.BI "-f" " traj.xtc "
-.TH g_dielectric 1 "Mon 22 Sep 2008"
+.TH g_dielectric 1 "Thu 16 Oct 2008"
.SH NAME
-g_dielectric
-.B VERSION 4.0_rc1
+g_dielectric - calculates frequency dependent dielectric constants
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_dielectric\fP
.BI "-f" " dipcorr.xvg "
-.TH g_dih 1 "Mon 22 Sep 2008"
+.TH g_dih 1 "Thu 16 Oct 2008"
.SH NAME
-g_dih
-.B VERSION 4.0_rc1
+g_dih - analyzes dihedral transitions
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_dih\fP
.BI "-f" " traj.xtc "
-.TH g_dipoles 1 "Mon 22 Sep 2008"
+.TH g_dipoles 1 "Thu 16 Oct 2008"
.SH NAME
-g_dipoles
-.B VERSION 4.0_rc1
+g_dipoles - computes the total dipole plus fluctuations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_dipoles\fP
.BI "-enx" " ener.edr "
-.TH g_disre 1 "Mon 22 Sep 2008"
+.TH g_disre 1 "Thu 16 Oct 2008"
.SH NAME
-g_disre
-.B VERSION 4.0_rc1
+g_disre - analyzes distance restraints
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_disre\fP
.BI "-s" " topol.tpr "
-.TH g_dist 1 "Mon 22 Sep 2008"
+.TH g_dist 1 "Thu 16 Oct 2008"
.SH NAME
-g_dist
-.B VERSION 4.0_rc1
+g_dist - calculates the distances between the centers of mass of two groups
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_dist\fP
.BI "-f" " traj.xtc "
-.TH g_dyndom 1 "Mon 22 Sep 2008"
+.TH g_dyndom 1 "Thu 16 Oct 2008"
.SH NAME
-g_dyndom
-.B VERSION 4.0_rc1
+g_dyndom - interpolate and extrapolate structure rotations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_dyndom\fP
.BI "-f" " dyndom.pdb "
-.TH g_enemat 1 "Mon 22 Sep 2008"
+.TH g_enemat 1 "Thu 16 Oct 2008"
.SH NAME
-g_enemat
-.B VERSION 4.0_rc1
+g_enemat - extracts an energy matrix from an energy file
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_enemat\fP
.BI "-f" " ener.edr "
-.TH g_energy 1 "Mon 22 Sep 2008"
+.TH g_energy 1 "Thu 16 Oct 2008"
.SH NAME
-g_energy
-.B VERSION 4.0_rc1
+g_energy - writes energies to xvg files and displays averages
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_energy\fP
.BI "-f" " ener.edr "
-.TH g_filter 1 "Mon 22 Sep 2008"
+.TH g_filter 1 "Thu 16 Oct 2008"
.SH NAME
-g_filter
-.B VERSION 4.0_rc1
+g_filter - frequency filters trajectories, useful for making smooth movies
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_filter\fP
.BI "-f" " traj.xtc "
-.TH g_gyrate 1 "Mon 22 Sep 2008"
+.TH g_gyrate 1 "Thu 16 Oct 2008"
.SH NAME
-g_gyrate
-.B VERSION 4.0_rc1
+g_gyrate - calculates the radius of gyration
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_gyrate\fP
.BI "-f" " traj.xtc "
-.TH g_h2order 1 "Mon 22 Sep 2008"
+.TH g_h2order 1 "Thu 16 Oct 2008"
.SH NAME
-g_h2order
-.B VERSION 4.0_rc1
+g_h2order - computes the orientation of water molecules
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_h2order\fP
.BI "-f" " traj.xtc "
-.TH g_hbond 1 "Mon 22 Sep 2008"
+.TH g_hbond 1 "Thu 16 Oct 2008"
.SH NAME
-g_hbond
-.B VERSION 4.0_rc1
+g_hbond - computes and analyzes hydrogen bonds
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_hbond\fP
.BI "-f" " traj.xtc "
-.TH g_helix 1 "Mon 22 Sep 2008"
+.TH g_helix 1 "Thu 16 Oct 2008"
.SH NAME
-g_helix
-.B VERSION 4.0_rc1
+g_helix - calculates basic properties of alpha helices
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_helix\fP
.BI "-s" " topol.tpr "
-.TH g_helixorient 1 "Mon 22 Sep 2008"
+.TH g_helixorient 1 "Thu 16 Oct 2008"
.SH NAME
-g_helixorient
-.B VERSION 4.0_rc1
+g_helixorient - calculates local pitch/bending/rotation/orientation inside helices
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_helixorient\fP
.BI "-s" " topol.tpr "
-.TH g_lie 1 "Mon 22 Sep 2008"
+.TH g_lie 1 "Thu 16 Oct 2008"
.SH NAME
-g_lie
-.B VERSION 4.0_rc1
+g_lie - free energy estimate from linear combinations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_lie\fP
.BI "-f" " ener.edr "
-.TH g_mdmat 1 "Mon 22 Sep 2008"
+.TH g_mdmat 1 "Thu 16 Oct 2008"
.SH NAME
-g_mdmat
-.B VERSION 4.0_rc1
+g_mdmat - calculates residue contact maps
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_mdmat\fP
.BI "-f" " traj.xtc "
-.TH g_mindist 1 "Mon 22 Sep 2008"
+.TH g_mindist 1 "Thu 16 Oct 2008"
.SH NAME
-g_mindist
-.B VERSION 4.0_rc1
+g_mindist - calculates the minimum distance between two groups
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_mindist\fP
.BI "-f" " traj.xtc "
-.TH g_morph 1 "Mon 22 Sep 2008"
+.TH g_morph 1 "Thu 16 Oct 2008"
.SH NAME
-g_morph
-.B VERSION 4.0_rc1
+g_morph - linear interpolation of conformations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_morph\fP
.BI "-f1" " conf1.gro "
-.TH g_msd 1 "Mon 22 Sep 2008"
+.TH g_msd 1 "Thu 16 Oct 2008"
.SH NAME
-g_msd
-.B VERSION 4.0_rc1
+g_msd - calculates mean square displacements
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_msd\fP
.BI "-f" " traj.xtc "
-.TH g_nmeig 1 "Mon 22 Sep 2008"
+.TH g_nmeig 1 "Thu 16 Oct 2008"
.SH NAME
-g_nmeig
-.B VERSION 4.0_rc1
+g_nmeig - diagonalizes the Hessian
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_nmeig\fP
.BI "-f" " hessian.mtx "
-.TH g_nmens 1 "Mon 22 Sep 2008"
+.TH g_nmens 1 "Thu 16 Oct 2008"
.SH NAME
-g_nmens
-.B VERSION 4.0_rc1
+g_nmens - generates an ensemble of structures from the normal modes
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_nmens\fP
.BI "-v" " eigenvec.trr "
-.TH g_nmtraj 1 "Mon 22 Sep 2008"
+.TH g_nmtraj 1 "Thu 16 Oct 2008"
.SH NAME
-g_nmtraj
-.B VERSION 4.0_rc1
+g_nmtraj - generate oscillating trajectory of an eigenmode
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_nmtraj\fP
.BI "-s" " topol.tpr "
-.TH g_order 1 "Mon 22 Sep 2008"
+.TH g_order 1 "Thu 16 Oct 2008"
.SH NAME
-g_order
-.B VERSION 4.0_rc1
+g_order - computes the order parameter per atom for carbon tails
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_order\fP
.BI "-f" " traj.xtc "
-.TH g_polystat 1 "Mon 22 Sep 2008"
+.TH g_polystat 1 "Thu 16 Oct 2008"
.SH NAME
-g_polystat
-.B VERSION 4.0_rc1
+g_polystat - calculates static properties of polymers
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_polystat\fP
.BI "-s" " topol.tpr "
-.TH g_potential 1 "Mon 22 Sep 2008"
+.TH g_potential 1 "Thu 16 Oct 2008"
.SH NAME
-g_potential
-.B VERSION 4.0_rc1
+g_potential - calculates the electrostatic potential across the box
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_potential\fP
.BI "-f" " traj.xtc "
-.TH g_principal 1 "Mon 22 Sep 2008"
+.TH g_principal 1 "Thu 16 Oct 2008"
.SH NAME
-g_principal
-.B VERSION 4.0_rc1
+g_principal - calculates axes of inertia for a group of atoms
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_principal\fP
.BI "-f" " traj.xtc "
.BI "-dt" " time "
.BI "-tu" " enum "
.BI "-[no]w" ""
+.BI "-[no]foo" ""
.SH DESCRIPTION
-g_principal calculates the three principal axes of inertion for a group
+g_principal calculates the three principal axes of inertia for a group
of atoms.
.SH FILES
.BI "-f" " traj.xtc"
.BI "-[no]w" "no "
View output xvg, xpm, eps and pdb files
+.BI "-[no]foo" "no "
+ Dummy option to avoid empty array
+
-.TH g_rama 1 "Mon 22 Sep 2008"
+.TH g_rama 1 "Thu 16 Oct 2008"
.SH NAME
-g_rama
-.B VERSION 4.0_rc1
+g_rama - computes Ramachandran plots
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rama\fP
.BI "-f" " traj.xtc "
-.TH g_rdf 1 "Mon 22 Sep 2008"
+.TH g_rdf 1 "Thu 16 Oct 2008"
.SH NAME
-g_rdf
-.B VERSION 4.0_rc1
+g_rdf - calculates radial distribution functions
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rdf\fP
.BI "-f" " traj.xtc "
-.TH g_rms 1 "Mon 22 Sep 2008"
+.TH g_rms 1 "Thu 16 Oct 2008"
.SH NAME
-g_rms
-.B VERSION 4.0_rc1
+g_rms - calculates rmsd's with a reference structure and rmsd matrices
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rms\fP
.BI "-s" " topol.tpr "
-.TH g_rmsdist 1 "Mon 22 Sep 2008"
+.TH g_rmsdist 1 "Thu 16 Oct 2008"
.SH NAME
-g_rmsdist
-.B VERSION 4.0_rc1
+g_rmsdist - calculates atom pair distances averaged with power 2, -3 or -6
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rmsdist\fP
.BI "-f" " traj.xtc "
-.TH g_rmsf 1 "Mon 22 Sep 2008"
+.TH g_rmsf 1 "Thu 16 Oct 2008"
.SH NAME
-g_rmsf
-.B VERSION 4.0_rc1
+g_rmsf - calculates atomic fluctuations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rmsf\fP
.BI "-f" " traj.xtc "
-.TH g_rotacf 1 "Mon 22 Sep 2008"
+.TH g_rotacf 1 "Thu 16 Oct 2008"
.SH NAME
-g_rotacf
-.B VERSION 4.0_rc1
+g_rotacf - calculates the rotational correlation function for molecules
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_rotacf\fP
.BI "-f" " traj.xtc "
-.TH g_saltbr 1 "Mon 22 Sep 2008"
+.TH g_saltbr 1 "Thu 16 Oct 2008"
.SH NAME
-g_saltbr
-.B VERSION 4.0_rc1
+g_saltbr - computes salt bridges
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_saltbr\fP
.BI "-f" " traj.xtc "
-.TH g_sas 1 "Mon 22 Sep 2008"
+.TH g_sas 1 "Thu 16 Oct 2008"
.SH NAME
-g_sas
-.B VERSION 4.0_rc1
+g_sas - computes solvent accessible surface area
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_sas\fP
.BI "-f" " traj.xtc "
.BI "-qmax" " real "
.BI "-[no]f_index" ""
.BI "-minarea" " real "
+.BI "-[no]pbc" ""
.BI "-[no]prot" ""
.BI "-dgs" " real "
.SH DESCRIPTION
By default, periodic boundary conditions are taken into account,
this can be turned off using the
-.B -pbc
+.B -nopbc
option.
.BI "-minarea" " real" " 0.5 "
The minimum area (nm2) to count an atom as a surface atom when writing a position restraint file (see help)
+.BI "-[no]pbc" "yes "
+ Take periodicity into account
+
.BI "-[no]prot" "yes "
Output the protein to the connelly pdb file too
-.TH g_sdf 1 "Mon 22 Sep 2008"
+.TH g_sdf 1 "Thu 16 Oct 2008"
.SH NAME
-g_sdf
-.B VERSION 4.0_rc1
+g_sdf - calculates the spatial distribution function (faster than g_spatial)
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_sdf\fP
.BI "-f" " traj.xtc "
-.TH g_sgangle 1 "Mon 22 Sep 2008"
+.TH g_sgangle 1 "Thu 16 Oct 2008"
.SH NAME
-g_sgangle
-.B VERSION 4.0_rc1
+g_sgangle - computes the angle and distance between two groups
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_sgangle\fP
.BI "-f" " traj.xtc "
-.TH g_sham 1 "Mon 22 Sep 2008"
+.TH g_sham 1 "Thu 16 Oct 2008"
.SH NAME
-g_sham
-.B VERSION 4.0_rc1
+g_sham - read/write xmgr and xvgr data sets
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_sham\fP
.BI "-f" " graph.xvg "
-.TH g_sorient 1 "Mon 22 Sep 2008"
+.TH g_sorient 1 "Thu 16 Oct 2008"
.SH NAME
-g_sorient
-.B VERSION 4.0_rc1
+g_sorient - analyzes solvent orientation around solutes
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_sorient\fP
.BI "-f" " traj.xtc "
-.TH g_spatial 1 "Mon 22 Sep 2008"
+.TH g_spatial 1 "Thu 16 Oct 2008"
.SH NAME
-g_spatial
-.B VERSION 4.0_rc1
+g_spatial - calculates the spatial distribution function (more control than g_sdf)
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_spatial\fP
.BI "-f" " traj.xtc "
-.TH g_spol 1 "Mon 22 Sep 2008"
+.TH g_spol 1 "Thu 16 Oct 2008"
.SH NAME
-g_spol
-.B VERSION 4.0_rc1
+g_spol - analyzes solvent dipole orientation and polarization around solutes
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_spol\fP
.BI "-f" " traj.xtc "
-.TH g_tcaf 1 "Mon 22 Sep 2008"
+.TH g_tcaf 1 "Thu 16 Oct 2008"
.SH NAME
-g_tcaf
-.B VERSION 4.0_rc1
+g_tcaf - calculates viscosities of liquids
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_tcaf\fP
.BI "-f" " traj.trr "
-.TH g_traj 1 "Mon 22 Sep 2008"
+.TH g_traj 1 "Thu 16 Oct 2008"
.SH NAME
-g_traj
-.B VERSION 4.0_rc1
+g_traj - plots x, v and f of selected atoms/groups (and more) from a trajectory
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_traj\fP
.BI "-f" " traj.xtc "
-.TH g_vanhove 1 "Mon 22 Sep 2008"
+.TH g_vanhove 1 "Thu 16 Oct 2008"
.SH NAME
-g_vanhove
-.B VERSION 4.0_rc1
+g_vanhove - calculates Van Hove displacement functions
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_vanhove\fP
.BI "-f" " traj.xtc "
-.TH g_velacc 1 "Mon 22 Sep 2008"
+.TH g_velacc 1 "Thu 16 Oct 2008"
.SH NAME
-g_velacc
-.B VERSION 4.0_rc1
+g_velacc - calculates velocity autocorrelation functions
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_velacc\fP
.BI "-f" " traj.trr "
With option
.B -mol
-the momentum autocorrelation function of
+the velocity autocorrelation function of
molecules is calculated. In this case the index group should consist
of molecule numbers instead of atom numbers.
.SH FILES
Calculate the momentum autocorrelation function
.BI "-[no]mol" "no "
- Calculate the momentum acf of molecules
+ Calculate the velocity acf of molecules
.BI "-acflen" " int" " -1"
Length of the ACF, default is half the number of frames
-.TH g_wham 1 "Mon 22 Sep 2008"
+.TH g_wham 1 "Thu 16 Oct 2008"
.SH NAME
-g_wham
-.B VERSION 4.0_rc1
+g_wham - weighted histogram analysis after umbrella sampling
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3g_wham\fP
.BI "-o" " profile.xvg "
-.TH genbox 1 "Mon 22 Sep 2008"
+.TH genbox 1 "Thu 16 Oct 2008"
.SH NAME
-genbox
-.B VERSION 4.0_rc1
+genbox - solvates a system
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3genbox\fP
.BI "-cp" " protein.gro "
-.TH genconf 1 "Mon 22 Sep 2008"
+.TH genconf 1 "Thu 16 Oct 2008"
.SH NAME
-genconf
-.B VERSION 4.0_rc1
+genconf - multiplies a conformation in 'random' orientations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3genconf\fP
.BI "-f" " conf.gro "
-.TH genion 1 "Mon 22 Sep 2008"
+.TH genion 1 "Thu 16 Oct 2008"
.SH NAME
-genion
-.B VERSION 4.0_rc1
+genion - generates mono atomic ions on energetically favorable positions
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3genion\fP
.BI "-s" " topol.tpr "
-.TH genrestr 1 "Mon 22 Sep 2008"
+.TH genrestr 1 "Thu 16 Oct 2008"
.SH NAME
-genrestr
-.B VERSION 4.0_rc1
+genrestr - generates position restraints or distance restraints for index groups
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3genrestr\fP
.BI "-f" " conf.gro "
-.TH gmxcheck 1 "Mon 22 Sep 2008"
+.TH gmxcheck 1 "Thu 16 Oct 2008"
.SH NAME
-gmxcheck
-.B VERSION 4.0_rc1
+gmxcheck - checks and compares files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3gmxcheck\fP
.BI "-f" " traj.xtc "
-.TH gmxdump 1 "Mon 22 Sep 2008"
+.TH gmxdump 1 "Thu 16 Oct 2008"
.SH NAME
-gmxdump
-.B VERSION 4.0_rc1
+gmxdump - makes binary files human readable
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3gmxdump\fP
.BI "-s" " topol.tpr "
-.TH grompp 1 "Mon 22 Sep 2008"
+.TH grompp 1 "Thu 16 Oct 2008"
.SH NAME
-grompp
-.B VERSION 4.0_rc1
+grompp - makes a run input file
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3grompp\fP
.BI "-f" " grompp.mdp "
-.TH highway 1 "Mon 22 Sep 2008"
+.TH highway 1 "Thu 16 Oct 2008"
.SH NAME
-highway
-.B VERSION 4.0_rc1
+highway - X-windows gadget for highway simulations
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3highway\fP
.BI "-f" " highway.dat "
-.TH make_edi 1 "Mon 22 Sep 2008"
+.TH make_edi 1 "Thu 16 Oct 2008"
.SH NAME
-make_edi
-.B VERSION 4.0_rc1
+make_edi - generate input files for essential dynamics sampling
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3make_edi\fP
.BI "-f" " eigenvec.trr "
-.TH make_ndx 1 "Mon 22 Sep 2008"
+.TH make_ndx 1 "Thu 16 Oct 2008"
.SH NAME
-make_ndx
-.B VERSION 4.0_rc1
+make_ndx - makes index files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3make_ndx\fP
.BI "-f" " conf.gro "
-.TH mdrun 1 "Mon 22 Sep 2008"
+.TH mdrun 1 "Thu 16 Oct 2008"
.SH NAME
-mdrun
-.B VERSION 4.0_rc1
+mdrun - performs a simulation, do a normal mode analysis or an energy minimization
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3mdrun\fP
.BI "-s" " topol.tpr "
not compatible with the PME grid x dimension.
But the user should optimize npme. Performance statistics on this issue
are written at the end of the log file.
-For good load balancing at high parallelization,
-npme should be divisible by the number of PME nodes
+For good load balancing at high parallelization, the PME grid x and y
+dimensions should be divisible by the number of PME nodes
+(the simulation will run correctly also when this is not the case).
that do not generate exclusions, this check can be turned off
with the option
.B -noddcheck
-.B .
+.
When constraints are present, option
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.
+
+
+
+When mdrun is started with MPI, it does not run niced by default.
.SH FILES
.BI "-s" " topol.tpr"
.B Input
-.TH mk_angndx 1 "Mon 22 Sep 2008"
+.TH mk_angndx 1 "Thu 16 Oct 2008"
.SH NAME
-mk_angndx
-.B VERSION 4.0_rc1
+mk_angndx - generates index files for g_angle
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3mk_angndx\fP
.BI "-s" " topol.tpr "
-.TH ngmx 1 "Mon 22 Sep 2008"
+.TH ngmx 1 "Thu 16 Oct 2008"
.SH NAME
-ngmx
-.B VERSION 4.0_rc1
+ngmx - displays a trajectory
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3ngmx\fP
.BI "-f" " traj.xtc "
-.TH pdb2gmx 1 "Mon 22 Sep 2008"
+.TH pdb2gmx 1 "Thu 16 Oct 2008"
.SH NAME
-pdb2gmx
-.B VERSION 4.0_rc1
+pdb2gmx - converts pdb files to topology and coordinate files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3pdb2gmx\fP
.BI "-f" " eiwit.pdb "
-.TH protonate 1 "Mon 22 Sep 2008"
+.TH protonate 1 "Thu 16 Oct 2008"
.SH NAME
-protonate
-.B VERSION 4.0_rc1
+protonate - protonates structures
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3protonate\fP
.BI "-s" " topol.tpr "
-.TH sigeps 1 "Mon 22 Sep 2008"
+.TH sigeps 1 "Thu 16 Oct 2008"
.SH NAME
-sigeps
-.B VERSION 4.0_rc1
+sigeps - convert c6/12 or c6/cn combinations to and from sigma/epsilon
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3sigeps\fP
.BI "-o" " potje.xvg "
-.TH tpbconv 1 "Mon 22 Sep 2008"
+.TH tpbconv 1 "Thu 16 Oct 2008"
.SH NAME
-tpbconv
-.B VERSION 4.0_rc1
+tpbconv - makes a run input file for restarting a crashed run
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3tpbconv\fP
.BI "-s" " topol.tpr "
-.TH trjcat 1 "Mon 22 Sep 2008"
+.TH trjcat 1 "Thu 16 Oct 2008"
.SH NAME
-trjcat
-.B VERSION 4.0_rc1
+trjcat - concatenates trajectory files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3trjcat\fP
.BI "-f" " traj.xtc "
-.TH trjconv 1 "Mon 22 Sep 2008"
+.TH trjconv 1 "Thu 16 Oct 2008"
.SH NAME
-trjconv
-.B VERSION 4.0_rc1
+trjconv - converts and manipulates trajectory files
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3trjconv\fP
.BI "-f" " traj.xtc "
-.TH trjorder 1 "Mon 22 Sep 2008"
+.TH trjorder 1 "Thu 16 Oct 2008"
.SH NAME
-trjorder
-.B VERSION 4.0_rc1
+trjorder - orders molecules according to their distance to a group
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3trjorder\fP
.BI "-f" " traj.xtc "
-.TH wheel 1 "Mon 22 Sep 2008"
+.TH wheel 1 "Thu 16 Oct 2008"
.SH NAME
-wheel
-.B VERSION 4.0_rc1
+wheel - plots helical wheels
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3wheel\fP
.BI "-f" " nnnice.dat "
-.TH x2top 1 "Mon 22 Sep 2008"
+.TH x2top 1 "Thu 16 Oct 2008"
.SH NAME
-x2top
-.B VERSION 4.0_rc1
+x2top - generates a primitive topology from coordinates
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3x2top\fP
.BI "-f" " conf.gro "
-.TH xpm2ps 1 "Mon 22 Sep 2008"
+.TH xpm2ps 1 "Thu 16 Oct 2008"
.SH NAME
-xpm2ps
-.B VERSION 4.0_rc1
+xpm2ps - convert XPM (XPixelMap) file to postscript
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3xpm2ps\fP
.BI "-f" " root.xpm "
-.TH xrama 1 "Mon 22 Sep 2008"
+.TH xrama 1 "Thu 16 Oct 2008"
.SH NAME
-xrama
-.B VERSION 4.0_rc1
+xrama - shows animated Ramachandran plots
+
+.B VERSION 4.0
.SH SYNOPSIS
\f3xrama\fP
.BI "-f" " traj.xtc "
biod.pnpi.spb.ru / alexxy / gromacs.git / commitdiff