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…
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…
g_dipoles – computes the total dipole plus fluctuations VERSION 4.0.1 Synopsisg_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 -[no]xvgr -mu…
g_dipoles – computes the total dipole plus fluctuations VERSION 4.0.1 Synopsisg_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 -[no]xvgr -mu…
g_dih – analyzes dihedral transitions VERSION 4.0.1 Synopsisg_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 Descriptiong_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 whole trajectory. When…
g_dih – analyzes dihedral transitions VERSION 4.0.1 Synopsisg_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 Descriptiong_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 whole trajectory. When…
g_dielectric – calculates frequency dependent dielectric constants VERSION 4.0.1 Synopsisg_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 -nsmooth int…
g_dielectric – calculates frequency dependent dielectric constants VERSION 4.0.1 Synopsisg_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 -nsmooth int…