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.
NAME g_vanhove – calculates Van Hove displacement functions VERSION 4.0.1 SYNOPSIS g_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…
NAME trjorder – orders molecules according to their distance to a group VERSION 4.0.1 SYNOPSIS trjorder -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 DESCRIPTION trjorder orders molecules according to the smallest distance to atoms in…
NAME trjorder – orders molecules according to their distance to a group VERSION 4.0.1 SYNOPSIS trjorder -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 DESCRIPTION trjorder orders molecules according to the smallest distance to atoms in…
NAME trjconv – converts and manipulates trajectory files VERSION 4.0.1 SYNOPSIS trjconv -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…
NAME trjconv – converts and manipulates trajectory files VERSION 4.0.1 SYNOPSIS trjconv -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…
NAME trjcat – concatenates trajectory files VERSION 4.0.1 SYNOPSIS trjcat -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 DESCRIPTION trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one…
NAME trjcat – concatenates trajectory files VERSION 4.0.1 SYNOPSIS trjcat -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 DESCRIPTION trjcat concatenates several input trajectory files in sorted order. In case of double time frames the one…
NAME g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 SYNOPSIS g_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…
NAME g_traj – plots x, v and f of selected atoms/groups (and more) from a trajectory VERSION 4.0.1 SYNOPSIS g_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…
NAME tpbconv – makes a run input file for restarting a crashed run VERSION 4.0.1 SYNOPSIS tpbconv -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 DESCRIPTION tpbconv can edit run input files in four ways. 1st. by modifying…
NAME tpbconv – makes a run input file for restarting a crashed run VERSION 4.0.1 SYNOPSIS tpbconv -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 DESCRIPTION tpbconv can edit run input files in four ways. 1st. by modifying…
NAME g_tcaf – calculates viscosities of liquids VERSION 4.0.1 SYNOPSIS g_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…
NAME g_tcaf – calculates viscosities of liquids VERSION 4.0.1 SYNOPSIS g_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…
NAME g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION g_spol analyzes dipoles around a solute; it is especially…
NAME g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION g_spol analyzes dipoles around a solute; it is especially…
NAME g_spatial – calculates the spatial distribution function (more control than g_sdf) VERSION 4.0.1 SYNOPSIS g_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…
NAME g_spatial – calculates the spatial distribution function (more control than g_sdf) VERSION 4.0.1 SYNOPSIS g_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…
NAME g_sorient – analyzes solvent orientation around solutes VERSION 4.0.1 SYNOPSIS g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc DESCRIPTION g_sorient analyzes solvent orientation…
NAME g_sorient – analyzes solvent orientation around solutes VERSION 4.0.1 SYNOPSIS g_sorient -f traj.xtc -s topol.tpr -n index.ndx -o sori.xvg -no snor.xvg -ro sord.xvg -co scum.xvg -rc scount.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]com -[no]v23 -rmin real -rmax real -cbin real -rbin real -[no]pbc DESCRIPTION g_sorient analyzes solvent orientation…
NAME sigeps – convert c6/12 or c6/cn combinations to and from sigma/epsilon VERSION 4.0.1 SYNOPSIS sigeps -o potje.xvg -[no]h -nice int -[no]w -[no]xvgr -c6 real -cn real -pow int -sig real -eps real -A real -B real -C real -qi real -qj real -sigfac real DESCRIPTION Sigeps is a simple utility that converts c6/c12 or…