genconf – multiplies a conformation in ‘random’ orientations VERSION 4.0.1 Synopsisgenconf -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 Descriptiongenconf multiplies a given coordinate file by simply stacking them on top of each other, like a small child…
genbox – solvates a system VERSION 4.0.1 Synopsisgenbox -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 DescriptionGenbox can do one of 3 things: 1) Generate a box of solvent. Specify -cs and -box. Or specify…
genbox – solvates a system VERSION 4.0.1 Synopsisgenbox -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 DescriptionGenbox can do one of 3 things: 1) Generate a box of solvent. Specify -cs and -box. Or specify…
g_filter – frequency filters trajectories, useful for making smooth movies VERSION 4.0.1 Synopsisg_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 Descriptiong_filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) + 1 from -A…
g_filter – frequency filters trajectories, useful for making smooth movies VERSION 4.0.1 Synopsisg_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 Descriptiong_filter performs frequency filtering on a trajectory. The filter shape is cos(pi t/A) + 1 from -A…
g_energy – writes energies to xvg files and displays averages VERSION 4.0.1 Synopsisg_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 -fetemp real…
g_energy – writes energies to xvg files and displays averages VERSION 4.0.1 Synopsisg_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 -fetemp real…
g_enemat – extracts an energy matrix from an energy file VERSION 4.0.1 Synopsisg_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 -temp real…
g_enemat – extracts an energy matrix from an energy file VERSION 4.0.1 Synopsisg_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 -temp real…
eneconv – converts energy files VERSION 4.0.1 Synopsiseneconv -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 DescriptionWith multiple files specified for the -f option: Concatenates several energy files in sorted order. In case of double time frames the one in the later file…
eneconv – converts energy files VERSION 4.0.1 Synopsiseneconv -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 DescriptionWith multiple files specified for the -f option: Concatenates several energy files in sorted order. In case of double time frames the one in the later file…
editconf – edits the box and writes subgroups VERSION 4.0.1 Synopsiseditconf -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 -[no]vdwread -[no]atom…
editconf – edits the box and writes subgroups VERSION 4.0.1 Synopsiseditconf -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 -[no]vdwread -[no]atom…
g_dyndom – interpolate and extrapolate structure rotations VERSION 4.0.1 Synopsisg_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 Descriptiong_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 axis furthermore it…
g_dyndom – interpolate and extrapolate structure rotations VERSION 4.0.1 Synopsisg_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 Descriptiong_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 axis furthermore it…
do_dssp – assigns secondary structure and calculates solvent accessible surface area VERSION 4.0.1 Synopsisdo_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 Descriptiondo_dssp reads a trajectory file and…
do_dssp – assigns secondary structure and calculates solvent accessible surface area VERSION 4.0.1 Synopsisdo_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 Descriptiondo_dssp reads a trajectory file and…
g_dist – calculates the distances between the centers of mass of two groups VERSION 4.0.1 Synopsisg_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 Descriptiong_dist can calculate the distance between the centers of mass of two groups of atoms as a…
g_dist – calculates the distances between the centers of mass of two groups VERSION 4.0.1 Synopsisg_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 Descriptiong_dist can calculate the distance between the centers of mass of two groups of atoms as a…
g_disre – analyzes distance restraints VERSION 4.0.1 Synopsisg_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 Descriptiong_disre computes violations of distance…