tpbconv – makes a run input file for restarting a crashed run VERSION 4.0.1 Synopsistpbconv -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 Descriptiontpbconv can edit run input files in four ways. 1st. by modifying the number of…
g_tcaf – calculates viscosities of liquids VERSION 4.0.1 Synopsisg_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 -endfit real…
g_tcaf – calculates viscosities of liquids VERSION 4.0.1 Synopsisg_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 -endfit real…
g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 Synopsisg_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 Descriptiong_spol analyzes dipoles around a solute; it is especially useful for polarizable…
g_spol – analyzes solvent dipole orientation and polarization around solutes VERSION 4.0.1 Synopsisg_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 Descriptiong_spol analyzes dipoles around a solute; it is especially useful for polarizable…
g_spatial – calculates the spatial distribution function (more control than g_sdf) VERSION 4.0.1 Synopsisg_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 -[no]dista -nlevels…
g_spatial – calculates the spatial distribution function (more control than g_sdf) VERSION 4.0.1 Synopsisg_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 -[no]dista -nlevels…
g_sorient – analyzes solvent orientation around solutes VERSION 4.0.1 Synopsisg_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 Descriptiong_sorient analyzes solvent orientation around solutes. It…
g_sorient – analyzes solvent orientation around solutes VERSION 4.0.1 Synopsisg_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 Descriptiong_sorient analyzes solvent orientation around solutes. It…
sigeps – convert c6/12 or c6/cn combinations to and from sigma/epsilon VERSION 4.0.1 Synopsissigeps -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 DescriptionSigeps is a simple utility that converts c6/c12 or c6/cn combinations to…
sigeps – convert c6/12 or c6/cn combinations to and from sigma/epsilon VERSION 4.0.1 Synopsissigeps -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 DescriptionSigeps is a simple utility that converts c6/c12 or c6/cn combinations to…
g_sham – read/write xmgr and xvgr data sets VERSION 4.0.1 Synopsisg_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg -g shamlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -ttol real -n int -[no]d -bw…
g_sham – read/write xmgr and xvgr data sets VERSION 4.0.1 Synopsisg_sham -f graph.xvg -ge gibbs.xvg -ene esham.xvg -dist ener.xvg -histo edist.xvg -bin bindex.ndx -lp prob.xpm -ls gibbs.xpm -lsh enthalpy.xpm -lss entropy.xpm -map map.xpm -ls3 gibbs3.pdb -mdata mapdata.xvg -g shamlog.log -[no]h -nice int -[no]w -[no]xvgr -[no]time -b real -e real -ttol real -n int -[no]d -bw…
g_sgangle – computes the angle and distance between two groups VERSION 4.0.1 Synopsisg_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]one -[no]z DescriptionCompute the angle and distance between two groups. The groups are defined by a number…
g_sgangle – computes the angle and distance between two groups VERSION 4.0.1 Synopsisg_sgangle -f traj.xtc -n index.ndx -s topol.tpr -oa sg_angle.xvg -od sg_dist.xvg -od1 sg_dist1.xvg -od2 sg_dist2.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -[no]one -[no]z DescriptionCompute the angle and distance between two groups. The groups are defined by a number…
g_sdf – calculates the spatial distribution function (faster than g_spatial) VERSION 4.0.1 Synopsisg_sdf -f traj.xtc -n index.ndx -s topol.tpr -o gom_plt.dat -r refmol.gro -[no]h -nice int -b time -e time -dt time -mode int -triangle vector -dtri vector -bin real -grid vector Descriptiong_sdf calculates the spatial distribution function (SDF) of a set of atoms within…
g_sdf – calculates the spatial distribution function (faster than g_spatial) VERSION 4.0.1 Synopsisg_sdf -f traj.xtc -n index.ndx -s topol.tpr -o gom_plt.dat -r refmol.gro -[no]h -nice int -b time -e time -dt time -mode int -triangle vector -dtri vector -bin real -grid vector Descriptiong_sdf calculates the spatial distribution function (SDF) of a set of atoms within…
g_sas – computes solvent accessible surface area VERSION 4.0.1 Synopsisg_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real Descriptiong_sas computes hydrophobic,…
g_sas – computes solvent accessible surface area VERSION 4.0.1 Synopsisg_sas -f traj.xtc -s topol.tpr -o area.xvg -or resarea.xvg -oa atomarea.xvg -tv volume.xvg -q connelly.pdb -n index.ndx -i surfat.itp -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -probe real -ndots int -qmax real -[no]f_index -minarea real -[no]pbc -[no]prot -dgs real Descriptiong_sas computes hydrophobic,…
g_saltbr – computes salt bridges VERSION 4.0.1 Synopsisg_saltbr -f traj.xtc -s topol.tpr -[no]h -nice int -b time -e time -dt time -t real -[no]sep Descriptiong_saltbr plots the distance between all combination of charged groups as a function of time. The groups are combined in different ways.A minimum distance can be given, (eg. the cut-off), then…