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_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…
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…
NAME do_dssp – assigns secondary structure and calculates solvent accessible surface area VERSION 4.0.1 SYNOPSIS do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -sss string DESCRIPTION do_dssp reads a…
NAME do_dssp – assigns secondary structure and calculates solvent accessible surface area VERSION 4.0.1 SYNOPSIS do_dssp -f traj.xtc -s topol.tpr -n index.ndx -ssdump ssdump.dat -map ss.map -o ss.xpm -sc scount.xvg -a area.xpm -ta totarea.xvg -aa averarea.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -sss string DESCRIPTION do_dssp reads a…
NAME g_dist – calculates the distances between the centers of mass of two groups VERSION 4.0.1 SYNOPSIS g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt lifetime.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -dist real DESCRIPTION g_dist can calculate the distance between the centers of mass of two groups of…
NAME g_dist – calculates the distances between the centers of mass of two groups VERSION 4.0.1 SYNOPSIS g_dist -f traj.xtc -s topol.tpr -n index.ndx -o dist.xvg -lt lifetime.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -dist real DESCRIPTION g_dist can calculate the distance between the centers of mass of two groups of…
NAME g_disre – analyzes distance restraints VERSION 4.0.1 SYNOPSIS g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -x matrix.xpm -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -ntop int -maxdr real -nlevels int -[no]third DESCRIPTION g_disre computes…
NAME g_disre – analyzes distance restraints VERSION 4.0.1 SYNOPSIS g_disre -s topol.tpr -f traj.xtc -ds drsum.xvg -da draver.xvg -dn drnum.xvg -dm drmax.xvg -dr restr.xvg -l disres.log -n viol.ndx -q viol.pdb -c clust.ndx -x matrix.xpm -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -ntop int -maxdr real -nlevels int -[no]third DESCRIPTION g_disre computes…
NAME g_dipoles – computes the total dipole plus fluctuations VERSION 4.0.1 SYNOPSIS g_dipoles -enx ener.edr -f traj.xtc -s topol.tpr -n index.ndx -o Mtot.xvg -eps epsilon.xvg -a aver.xvg -d dipdist.xvg -c dipcorr.xvg -g gkr.xvg -adip adip.xvg -dip3d dip3d.xvg -cos cosaver.xvg -cmap cmap.xpm -q quadrupole.xvg -slab slab.xvg -[no]h -nice int -b time -e time -dt time -[no]w…
NAME g_dipoles – computes the total dipole plus fluctuations VERSION 4.0.1 SYNOPSIS g_dipoles -enx ener.edr -f traj.xtc -s topol.tpr -n index.ndx -o Mtot.xvg -eps epsilon.xvg -a aver.xvg -d dipdist.xvg -c dipcorr.xvg -g gkr.xvg -adip adip.xvg -dip3d dip3d.xvg -cos cosaver.xvg -cmap cmap.xpm -q quadrupole.xvg -slab slab.xvg -[no]h -nice int -b time -e time -dt time -[no]w…
NAME g_dih – analyzes dihedral transitions VERSION 4.0.1 SYNOPSIS g_dih -f traj.xtc -s topol.tpr -o hello.out -[no]h -nice int -b time -e time -dt time -[no]w -[no]sa -mult int DESCRIPTION g_dih can do two things. The default is to analyze dihedral transitions by merely computing all the dihedral angles defined in your topology for the…
NAME g_dih – analyzes dihedral transitions VERSION 4.0.1 SYNOPSIS g_dih -f traj.xtc -s topol.tpr -o hello.out -[no]h -nice int -b time -e time -dt time -[no]w -[no]sa -mult int DESCRIPTION g_dih can do two things. The default is to analyze dihedral transitions by merely computing all the dihedral angles defined in your topology for the…
NAME g_dielectric – calculates frequency dependent dielectric constants VERSION 4.0.1 SYNOPSIS g_dielectric -f dipcorr.xvg -d deriv.xvg -o epsw.xvg -c cole.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]fft -[no]x1 -eint real -bfit real -efit real -tail real -A real -tau1 real -tau2 real -eps0 real -epsRF real -fix int -ffn enum…