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 gmxcheck – checks and compares files VERSION 4.0.1 SYNOPSIS gmxcheck -f traj.xtc -f2 traj.xtc -s1 top1.tpr -s2 top2.tpr -c topol.tpr -e ener.edr -e2 ener2.edr -n index.ndx -m doc.tex -[no]h -nice int -vdwfac real -bonlo real -bonhi real -tol real -[no]ab -lastener string DESCRIPTION gmxcheck reads a trajectory ( .trj, .trr or .xtc), an energy…
NAME genrestr – generates position restraints or distance restraints for index groups VERSION 4.0.1 SYNOPSIS genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -[no]constr DESCRIPTION genrestr produces an include file for a topology containing a list of atom numbers and…
NAME genrestr – generates position restraints or distance restraints for index groups VERSION 4.0.1 SYNOPSIS genrestr -f conf.gro -n index.ndx -o posre.itp -of freeze.ndx -[no]h -nice int -fc vector -freeze real -[no]disre -disre_dist real -disre_frac real -disre_up2 real -[no]constr DESCRIPTION genrestr produces an include file for a topology containing a list of atom numbers and…
NAME genion – generates mono atomic ions on energetically favorable positions VERSION 4.0.1 SYNOPSIS genion -s topol.tpr -table table.xvg -n index.ndx -o out.gro -g genion.log -pot pot.pdb -p topol.top -[no]h -nice int -[no]xvgr -np int -pname string -pq int -nn int -nname string -nq int -rmin real -[no]random -seed int -scale real -conc real -[no]neutral…
NAME genion – generates mono atomic ions on energetically favorable positions VERSION 4.0.1 SYNOPSIS genion -s topol.tpr -table table.xvg -n index.ndx -o out.gro -g genion.log -pot pot.pdb -p topol.top -[no]h -nice int -[no]xvgr -np int -pname string -pq int -nn int -nname string -nq int -rmin real -[no]random -seed int -scale real -conc real -[no]neutral…
NAME genconf – multiplies a conformation in ‘random’ orientations VERSION 4.0.1 SYNOPSIS genconf -f conf.gro -o out.gro -trj traj.xtc -[no]h -nice int -nbox vector -dist vector -seed int -[no]rot -[no]shuffle -[no]sort -block int -nmolat int -maxrot vector -[no]renumber DESCRIPTION genconf multiplies a given coordinate file by simply stacking them on top of each other, like…
NAME genconf – multiplies a conformation in ‘random’ orientations VERSION 4.0.1 SYNOPSIS genconf -f conf.gro -o out.gro -trj traj.xtc -[no]h -nice int -nbox vector -dist vector -seed int -[no]rot -[no]shuffle -[no]sort -block int -nmolat int -maxrot vector -[no]renumber DESCRIPTION genconf multiplies a given coordinate file by simply stacking them on top of each other, like…
NAME genbox – solvates a system VERSION 4.0.1 SYNOPSIS genbox -cp protein.gro -cs spc216.gro -ci insert.gro -o out.gro -p topol.top -[no]h -nice int -box vector -nmol int -try int -seed int -vdwd real -shell real -maxsol int -[no]vel DESCRIPTION Genbox can do one of 3 things: 1) Generate a box of solvent. Specify -cs and…
NAME genbox – solvates a system VERSION 4.0.1 SYNOPSIS genbox -cp protein.gro -cs spc216.gro -ci insert.gro -o out.gro -p topol.top -[no]h -nice int -box vector -nmol int -try int -seed int -vdwd real -shell real -maxsol int -[no]vel DESCRIPTION Genbox can do one of 3 things: 1) Generate a box of solvent. Specify -cs and…
NAME g_filter – frequency filters trajectories, useful for making smooth movies VERSION 4.0.1 SYNOPSIS g_filter -f traj.xtc -s topol.tpr -n index.ndx -ol lowpass.xtc -oh highpass.xtc -[no]h -nice int -b time -e time -dt time -[no]w -nf int -[no]all -[no]nojump -[no]fit DESCRIPTION g_filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) +…
NAME g_filter – frequency filters trajectories, useful for making smooth movies VERSION 4.0.1 SYNOPSIS g_filter -f traj.xtc -s topol.tpr -n index.ndx -ol lowpass.xtc -oh highpass.xtc -[no]h -nice int -b time -e time -dt time -[no]w -nf int -[no]all -[no]nojump -[no]fit DESCRIPTION g_filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) +…
NAME g_energy – writes energies to xvg files and displays averages VERSION 4.0.1 SYNOPSIS g_energy -f ener.edr -f2 ener.edr -s topol.tpr -o energy.xvg -viol violaver.xvg -pairs pairs.xvg -ora orienta.xvg -ort orientt.xvg -oda orideva.xvg -odr oridevr.xvg -odt oridevt.xvg -oten oriten.xvg -corr enecorr.xvg -vis visco.xvg -ravg runavgdf.xvg -[no]h -nice int -b time -e time -[no]w -[no]xvgr -[no]fee…
NAME g_energy – writes energies to xvg files and displays averages VERSION 4.0.1 SYNOPSIS g_energy -f ener.edr -f2 ener.edr -s topol.tpr -o energy.xvg -viol violaver.xvg -pairs pairs.xvg -ora orienta.xvg -ort orientt.xvg -oda orideva.xvg -odr oridevr.xvg -odt oridevt.xvg -oten oriten.xvg -corr enecorr.xvg -vis visco.xvg -ravg runavgdf.xvg -[no]h -nice int -b time -e time -[no]w -[no]xvgr -[no]fee…
NAME g_enemat – extracts an energy matrix from an energy file VERSION 4.0.1 SYNOPSIS g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]sum -skip int -[no]mean -nlevels int -max real -min real -[no]coul -[no]coulr -[no]coul14 -[no]lj -[no]lj -[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free…
NAME g_enemat – extracts an energy matrix from an energy file VERSION 4.0.1 SYNOPSIS g_enemat -f ener.edr -groups groups.dat -eref eref.dat -emat emat.xpm -etot energy.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]sum -skip int -[no]mean -nlevels int -max real -min real -[no]coul -[no]coulr -[no]coul14 -[no]lj -[no]lj -[no]lj14 -[no]bhamsr -[no]bhamlr -[no]free…
NAME eneconv – converts energy files VERSION 4.0.1 SYNOPSIS eneconv -f ener.edr -o fixed.edr -[no]h -nice int -b real -e real -dt real -offset real -[no]settime -[no]sort -scalefac real -[no]error DESCRIPTION With multiple files specified for the -f option: Concatenates several energy files in sorted order. In case of double time frames the one in…
NAME eneconv – converts energy files VERSION 4.0.1 SYNOPSIS eneconv -f ener.edr -o fixed.edr -[no]h -nice int -b real -e real -dt real -offset real -[no]settime -[no]sort -scalefac real -[no]error DESCRIPTION With multiple files specified for the -f option: Concatenates several energy files in sorted order. In case of double time frames the one in…
NAME editconf – edits the box and writes subgroups VERSION 4.0.1 SYNOPSIS editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf bfact.dat -[no]h -nice int -[no]w -[no]ndef -bt enum -box vector -angles vector -d real -[no]c -center vector -translate vector -rotate vector -[no]princ -scale vector -density real -[no]vol -[no]pbc -[no]grasp -rvdw real -sig56 real…
NAME editconf – edits the box and writes subgroups VERSION 4.0.1 SYNOPSIS editconf -f conf.gro -n index.ndx -o out.gro -mead mead.pqr -bf bfact.dat -[no]h -nice int -[no]w -[no]ndef -bt enum -box vector -angles vector -d real -[no]c -center vector -translate vector -rotate vector -[no]princ -scale vector -density real -[no]vol -[no]pbc -[no]grasp -rvdw real -sig56 real…
NAME g_dyndom – interpolate and extrapolate structure rotations VERSION 4.0.1 SYNOPSIS g_dyndom -f dyndom.pdb -o rotated.xtc -n domains.ndx -[no]h -nice int -firstangle real -lastangle real -nframe int -maxangle real -trans real -head vector -tail vector DESCRIPTION g_dyndom reads a pdb file output from DynDom http://www.cmp.uea.ac.uk/dyndom/ It reads the coordinates, and the coordinates of the rotation…