Section 1: user commands and tools
NAME g_saltbr – computes salt bridges VERSION 4.0.1 SYNOPSIS g_saltbr -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time -t real -[no]sep DESCRIPTION g_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg….
NAME g_saltbr – computes salt bridges VERSION 4.0.1 SYNOPSIS g_saltbr -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time -t real -[no]sep DESCRIPTION g_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg….
NAME g_rotacf – calculates the rotational correlation function for molecules VERSION 4.0.1 SYNOPSIS g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_rotacf calculates the rotational correlation function…
NAME g_rotacf – calculates the rotational correlation function for molecules VERSION 4.0.1 SYNOPSIS g_rotacf -f traj.xtc -s topol.tpr -n index.ndx -o rotacf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]d -[no]aver -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_rotacf calculates the rotational correlation function…
NAME g_rmsf – calculates atomic fluctuations VERSION 4.0.1 SYNOPSIS g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res -[no]aniso -[no]fit DESCRIPTION g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard…
NAME g_rmsf – calculates atomic fluctuations VERSION 4.0.1 SYNOPSIS g_rmsf -f traj.xtc -s topol.tpr -n index.ndx -q eiwit.pdb -oq bfac.pdb -ox xaver.pdb -o rmsf.xvg -od rmsdev.xvg -oc correl.xvg -dir rmsf.log -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]res -[no]aniso -[no]fit DESCRIPTION g_rmsf computes the root mean square fluctuation (RMSF, i.e. standard…
NAME g_rmsdist – calculates atom pair distances averaged with power 2, -3 or -6 VERSION 4.0.1 SYNOPSIS g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real…
NAME g_rmsdist – calculates atom pair distances averaged with power 2, -3 or -6 VERSION 4.0.1 SYNOPSIS g_rmsdist -f traj.xtc -s topol.tpr -n index.ndx -equiv equiv.dat -o distrmsd.xvg -rms rmsdist.xpm -scl rmsscale.xpm -mean rmsmean.xpm -nmr3 nmr3.xpm -nmr6 nmr6.xpm -noe noe.dat -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nlevels int -max real…
NAME g_rms – calculates rmsd’s with a reference structure and rmsd matrices VERSION 4.0.1 SYNOPSIS g_rms -s topol.tpr -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg -mir rmsdmir.xvg -a avgrp.xvg -dist rmsd-dist.xvg -m rmsd.xpm -bin rmsd.dat -bm bond.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -what enum -[no]pbc -fit…
NAME g_rms – calculates rmsd’s with a reference structure and rmsd matrices VERSION 4.0.1 SYNOPSIS g_rms -s topol.tpr -f traj.xtc -f2 traj.xtc -n index.ndx -o rmsd.xvg -mir rmsdmir.xvg -a avgrp.xvg -dist rmsd-dist.xvg -m rmsd.xpm -bin rmsd.dat -bm bond.xpm -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -what enum -[no]pbc -fit…
NAME g_rdf – calculates radial distribution functions VERSION 4.0.1 SYNOPSIS g_rdf -f traj.xtc -s topol.tpr -n index.ndx -o rdf.xvg -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -bin real -[no]com -rdf enum -[no]pbc -[no]norm -[no]xy -cut real -ng int -fade real -nlevel int -startq real -endq…
NAME g_rdf – calculates radial distribution functions VERSION 4.0.1 SYNOPSIS g_rdf -f traj.xtc -s topol.tpr -n index.ndx -o rdf.xvg -sq sq.xvg -cn rdf_cn.xvg -hq hq.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -bin real -[no]com -rdf enum -[no]pbc -[no]norm -[no]xy -cut real -ng int -fade real -nlevel int -startq real -endq…
NAME g_rama – computes Ramachandran plots VERSION 4.0.1 SYNOPSIS g_rama -f traj.xtc -s topol.tpr -o rama.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr DESCRIPTION g_rama selects the Phi/Psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you can…
NAME g_rama – computes Ramachandran plots VERSION 4.0.1 SYNOPSIS g_rama -f traj.xtc -s topol.tpr -o rama.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr DESCRIPTION g_rama selects the Phi/Psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you can…
NAME protonate – protonates structures VERSION 4.0.1 SYNOPSIS protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time DESCRIPTION protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb. If only -s is specified, this conformation will be protonated, if also -f is specified,…
NAME protonate – protonates structures VERSION 4.0.1 SYNOPSIS protonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time DESCRIPTION protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb. If only -s is specified, this conformation will be protonated, if also -f is specified,…
NAME g_principal – calculates axes of inertia for a group of atoms VERSION 4.0.1 SYNOPSIS g_principal -f traj.xtc -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]foo DESCRIPTION g_principal calculates the three principal axes of inertia for a group…
NAME g_principal – calculates axes of inertia for a group of atoms VERSION 4.0.1 SYNOPSIS g_principal -f traj.xtc -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]foo DESCRIPTION g_principal calculates the three principal axes of inertia for a group…
NAME g_potential – calculates the electrostatic potential across the box VERSION 4.0.1 SYNOPSIS g_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correct DESCRIPTION Compute the electrostatical…
NAME g_potential – calculates the electrostatic potential across the box VERSION 4.0.1 SYNOPSIS g_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correct DESCRIPTION Compute the electrostatical…