Section 1: user commands and tools
NAME g_hbond – computes and analyzes hydrogen bonds VERSION 4.0.1 SYNOPSIS g_hbond -f traj.xtc -s topol.tpr -n index.ndx -num hbnum.xvg -g hbond.log -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx hbhelix.xvg -hbn hbond.ndx -hbm hbmap.xpm -don donor.xvg -dan danum.xvg -life hblife.xvg -nhbdist nhbdist.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -[no]ins -a real…
NAME g_hbond – computes and analyzes hydrogen bonds VERSION 4.0.1 SYNOPSIS g_hbond -f traj.xtc -s topol.tpr -n index.ndx -num hbnum.xvg -g hbond.log -ac hbac.xvg -dist hbdist.xvg -ang hbang.xvg -hx hbhelix.xvg -hbn hbond.ndx -hbm hbmap.xpm -don donor.xvg -dan danum.xvg -life hblife.xvg -nhbdist nhbdist.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -[no]ins -a real…
NAME g_h2order – computes the orientation of water molecules VERSION 4.0.1 SYNOPSIS g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int DESCRIPTION Compute the orientation of water molecules with respect to the normal of the box. The program…
NAME g_h2order – computes the orientation of water molecules VERSION 4.0.1 SYNOPSIS g_h2order -f traj.xtc -n index.ndx -nm index.ndx -s topol.tpr -o order.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int DESCRIPTION Compute the orientation of water molecules with respect to the normal of the box. The program…
NAME g_gyrate – calculates the radius of gyration VERSION 4.0.1 SYNOPSIS g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nmol int -[no]q -[no]p -[no]moi -nz int -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_gyrate…
NAME g_gyrate – calculates the radius of gyration VERSION 4.0.1 SYNOPSIS g_gyrate -f traj.xtc -s topol.tpr -n index.ndx -o gyrate.xvg -acf moi-acf.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -nmol int -[no]q -[no]p -[no]moi -nz int -acflen int -[no]normalize -P enum -fitfn enum -ncskip int -beginfit real -endfit real DESCRIPTION g_gyrate…
NAME grompp – makes a run input file VERSION 4.0.1 SYNOPSIS grompp -f grompp.mdp -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro -n index.ndx -p topol.top -pp processed.top -o topol.tpr -t traj.trr -e ener.edr -[no]h -nice int -[no]v -time real -[no]rmvsbds -maxwarn int -[no]zero -[no]renum DESCRIPTION The gromacs preprocessor reads a molecular topology file, checks…
NAME grompp – makes a run input file VERSION 4.0.1 SYNOPSIS grompp -f grompp.mdp -po mdout.mdp -c conf.gro -r conf.gro -rb conf.gro -n index.ndx -p topol.top -pp processed.top -o topol.tpr -t traj.trr -e ener.edr -[no]h -nice int -[no]v -time real -[no]rmvsbds -maxwarn int -[no]zero -[no]renum DESCRIPTION The gromacs preprocessor reads a molecular topology file, checks…
NAME gmxdump – makes binary files human readable VERSION 4.0.1 SYNOPSIS gmxdump -s topol.tpr -f traj.xtc -e ener.edr -cp state.cpt -om grompp.mdp -[no]h -nice int -[no]nr DESCRIPTION gmxdump reads a run input file ( .tpa/ .tpr/ .tpb), a trajectory ( .trj/ .trr/ .xtc) or an energy file ( .ene/ .edr) and prints that to standard…
NAME gmxdump – makes binary files human readable VERSION 4.0.1 SYNOPSIS gmxdump -s topol.tpr -f traj.xtc -e ener.edr -cp state.cpt -om grompp.mdp -[no]h -nice int -[no]nr DESCRIPTION gmxdump reads a run input file ( .tpa/ .tpr/ .tpb), a trajectory ( .trj/ .trr/ .xtc) or an energy file ( .ene/ .edr) and prints that to standard…
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 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…