The Linux Manuals (man pages) document is an important part of Linux documents. Linux Manuals are organized as several sections. Each section has a group of commands for a specific area in Linux usage, administration or development.
g_wham – weighted histogram analysis after umbrella sampling VERSION 4.0.1 Synopsisg_wham -o profile.xvg -hist histo.xvg -[no]h -nice int -[no]w -[no]xvgr -min real -max real -bins int -[no]prof -temp real -[no]flip -tol real DescriptionThis is an analysis program that implements the Weighted Histogram Analysis Method (WHAM). It is intended to analyze .pdo files generated by mdrun…
g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 Synopsisg_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real Descriptiong_velacc computes the velocity autocorrelation function. When the -m option is used,…
g_velacc – calculates velocity autocorrelation functions VERSION 4.0.1 Synopsisg_velacc -f traj.trr -s topol.tpr -n index.ndx -o vac.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]m -[no]mol -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real Descriptiong_velacc computes the velocity autocorrelation function. When the -m option is used,…
g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 Synopsisg_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int Descriptiong_vanhove computes…
g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 Synopsisg_vanhove -f traj.xtc -s topol.tpr -n index.ndx -om vanhove.xpm -or vanhove_r.xvg -ot vanhove_t.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -sqrt real -fm int -rmax real -rbin real -mmax real -nlevels int -nr int -fr int -rt real -ft int Descriptiong_vanhove computes…
trjorder – orders molecules according to their distance to a group VERSION 4.0.1 Synopsistrjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int -da int -[no]com -r real Descriptiontrjorder orders molecules according to the smallest distance to atoms in a reference group….
trjorder – orders molecules according to their distance to a group VERSION 4.0.1 Synopsistrjorder -f traj.xtc -s topol.tpr -n index.ndx -o ordered.xtc -nshell nshell.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -na int -da int -[no]com -r real Descriptiontrjorder orders molecules according to the smallest distance to atoms in a reference group….
trjconv – converts and manipulates trajectory files VERSION 4.0.1 Synopsistrjconv -f traj.xtc -o trajout.xtc -s topol.tpr -n index.ndx -fr frames.ndx -sub cluster.ndx -drop drop.xvg -[no]h -nice int -b time -e time -tu enum -[no]w -[no]xvgr -skip int -dt time -dump time -t0 time -timestep time -pbc enum -ur enum -[no]center -boxcenter enum -box vector -trans…
trjconv – converts and manipulates trajectory files VERSION 4.0.1 Synopsistrjconv -f traj.xtc -o trajout.xtc -s topol.tpr -n index.ndx -fr frames.ndx -sub cluster.ndx -drop drop.xvg -[no]h -nice int -b time -e time -tu enum -[no]w -[no]xvgr -skip int -dt time -dump time -t0 time -timestep time -pbc enum -ur enum -[no]center -boxcenter enum -box vector -trans…
trjcat – concatenates trajectory files VERSION 4.0.1 Synopsistrjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -nice int -tu enum -[no]xvgr -b time -e time -dt time -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]cat Descriptiontrjcat concatenates several input trajectory files in sorted order. In case of double time frames the one in the later…
trjcat – concatenates trajectory files VERSION 4.0.1 Synopsistrjcat -f traj.xtc -o trajout.xtc -n index.ndx -demux remd.xvg -[no]h -nice int -tu enum -[no]xvgr -b time -e time -dt time -prec int -[no]vel -[no]settime -[no]sort -[no]keeplast -[no]cat Descriptiontrjcat concatenates several input trajectory files in sorted order. In case of double time frames the one in the later…
g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 Synopsisg_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -nice int -b time…
g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 Synopsisg_traj -f traj.xtc -s topol.tpr -n index.ndx -ox coord.xvg -oxt coord.xtc -ov veloc.xvg -of force.xvg -ob box.xvg -ot temp.xvg -ekt ektrans.xvg -ekr ekrot.xvg -vd veldist.xvg -cv veloc.pdb -cf force.pdb -av all_veloc.xvg -af all_force.xvg -[no]h -nice int -b time…
tpbconv – makes a run input file for restarting a crashed run VERSION 4.0.1 Synopsistpbconv -s topol.tpr -f traj.trr -e ener.edr -n index.ndx -o tpxout.tpr -[no]h -nice int -nsteps int -runtime real -time real -extend real -until real -[no]zeroq -[no]cont Descriptiontpbconv can edit run input files in four ways. 1st. by modifying the number of…
tpbconv – makes a run input file for restarting a crashed run VERSION 4.0.1 Synopsistpbconv -s topol.tpr -f traj.trr -e ener.edr -n index.ndx -o tpxout.tpr -[no]h -nice int -nsteps int -runtime real -time real -extend real -until real -[no]zeroq -[no]cont Descriptiontpbconv can edit run input files in four ways. 1st. by modifying the number of…
g_tcaf – calculates viscosities of liquids VERSION 4.0.1 Synopsisg_tcaf -f traj.trr -s topol.tpr -n index.ndx -ot transcur.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg -oc tcaf_cub.xvg -ov visc_k.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]mol -[no]k34 -wt real -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real…
g_tcaf – calculates viscosities of liquids VERSION 4.0.1 Synopsisg_tcaf -f traj.trr -s topol.tpr -n index.ndx -ot transcur.xvg -oa tcaf_all.xvg -o tcaf.xvg -of tcaf_fit.xvg -oc tcaf_cub.xvg -ov visc_k.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]mol -[no]k34 -wt real -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real…
g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 Synopsisg_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -refat int -rmin real -rmax real -dip real -bw real Descriptiong_spol analyzes dipoles around a solute; it is especially useful for polarizable…
g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 Synopsisg_spol -f traj.xtc -s topol.tpr -n index.ndx -o scdist.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -refat int -rmin real -rmax real -dip real -bw real Descriptiong_spol analyzes dipoles around a solute; it is especially useful for polarizable…
g_spatial – calculates the spatial distribution function (more control than g_sdf) VERSION 4.0.1 Synopsisg_spatial -f traj.xtc -s topol.tpr -n index.ndx -dm rmsd.xpm -o rmsd-clust.xpm -g cluster.log -dist rmsd-dist.xvg -ev rmsd-eig.xvg -sz clust-size.xvg -tr clust-trans.xpm -ntr clust-trans.xvg -clid clust-id.xvg -cl clusters.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]dista -nlevels…