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 mdrun – performs a simulation, do a normal mode analysis or an energy minimization VERSION 4.0.1 SYNOPSIS mdrun -s topol.tpr -o traj.trr -x traj.xtc -cpi state.cpt -cpo state.cpt -c confout.gro -e ener.edr -g md.log -dgdl dgdl.xvg -field field.xvg -table table.xvg -tablep tablep.xvg -tableb table.xvg -rerun rerun.xtc -tpi tpi.xvg -tpid tpidist.xvg -ei sam.edi -eo sam.edo…
NAME g_mdmat – calculates residue contact maps VERSION 4.0.1 SYNOPSIS g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -t real -nlevels int DESCRIPTION g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames these distance matrices…
NAME g_mdmat – calculates residue contact maps VERSION 4.0.1 SYNOPSIS g_mdmat -f traj.xtc -s topol.tpr -n index.ndx -mean dm.xpm -frames dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -t real -nlevels int DESCRIPTION g_mdmat makes distance matrices consisting of the smallest distance between residue pairs. With -frames these distance matrices…
NAME make_ndx – makes index files VERSION 4.0.1 SYNOPSIS make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -nice int -natoms int DESCRIPTION Index groups are necessary for almost every gromacs program. All these programs can generate default index groups. You ONLY have to use make_ndx when you need SPECIAL index groups. There is a default…
NAME make_ndx – makes index files VERSION 4.0.1 SYNOPSIS make_ndx -f conf.gro -n index.ndx -o index.ndx -[no]h -nice int -natoms int DESCRIPTION Index groups are necessary for almost every gromacs program. All these programs can generate default index groups. You ONLY have to use make_ndx when you need SPECIAL index groups. There is a default…
NAME make_edi – generate input files for essential dynamics sampling VERSION 4.0.1 SYNOPSIS make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -n index.ndx -tar target.gro -ori origin.gro -o sam.edi -[no]h -nice int -[no]xvgr -mon string -linfix string -linacc string -flood string -radfix string -radacc string -radcon string -outfrq int -slope real -maxedsteps int -deltaF0 real -deltaF…
NAME make_edi – generate input files for essential dynamics sampling VERSION 4.0.1 SYNOPSIS make_edi -f eigenvec.trr -eig eigenval.xvg -s topol.tpr -n index.ndx -tar target.gro -ori origin.gro -o sam.edi -[no]h -nice int -[no]xvgr -mon string -linfix string -linacc string -flood string -radfix string -radacc string -radcon string -outfrq int -slope real -maxedsteps int -deltaF0 real -deltaF…
NAME g_lie – free energy estimate from linear combinations VERSION 4.0.1 SYNOPSIS g_lie -f ener.edr -o lie.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -Elj real -Eqq real -Clj real -Cqq real -ligand string DESCRIPTION g_lie computes a free energy estimate based on an energy analysis from. One needs an energy…
NAME g_lie – free energy estimate from linear combinations VERSION 4.0.1 SYNOPSIS g_lie -f ener.edr -o lie.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -Elj real -Eqq real -Clj real -Cqq real -ligand string DESCRIPTION g_lie computes a free energy estimate based on an energy analysis from. One needs an energy…
NAME g_kinetics – derives information about kinetic processes from you trajectories VERSION 4.0.1 SYNOPSIS g_kinetics -f temp.xvg -d data.xvg -d2 data2.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -ee err_est.xvg -g remd.log -m melt.xvg -[no]h -nice int -tu enum -[no]w -[no]xvgr -[no]time -b real -e real -bfit real -efit real -T real -n int -cut real…
NAME g_kinetics – derives information about kinetic processes from you trajectories VERSION 4.0.1 SYNOPSIS g_kinetics -f temp.xvg -d data.xvg -d2 data2.xvg -o ft_all.xvg -o2 it_all.xvg -o3 ft_repl.xvg -ee err_est.xvg -g remd.log -m melt.xvg -[no]h -nice int -tu enum -[no]w -[no]xvgr -[no]time -b real -e real -bfit real -efit real -T real -n int -cut real…
NAME highway – X-windows gadget for highway simulations VERSION 4.0.1 SYNOPSIS highway -f highway.dat -[no]h -nice int DESCRIPTION highway is the gromacs highway simulator. It is an X-windows gadget that shows a (periodic) Autobahn with a user defined number of cars. Fog can be turned on or off to increase the number of crashes. Nice…
NAME highway – X-windows gadget for highway simulations VERSION 4.0.1 SYNOPSIS highway -f highway.dat -[no]h -nice int DESCRIPTION highway is the gromacs highway simulator. It is an X-windows gadget that shows a (periodic) Autobahn with a user defined number of cars. Fog can be turned on or off to increase the number of crashes. Nice…
NAME g_helixorient – calculates local pitch/bending/rotation/orientation inside helices VERSION 4.0.1 SYNOPSIS g_helixorient -s topol.tpr -f traj.xtc -n index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise rise.xvg -oradius radius.xvg -otwist twist.xvg -obending bending.xvg -otilt tilt.xvg -orot rotation.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -[no]sidechain -[no]incremental DESCRIPTION g_helixorient calculates coordinates and direction of the average…
NAME g_helixorient – calculates local pitch/bending/rotation/orientation inside helices VERSION 4.0.1 SYNOPSIS g_helixorient -s topol.tpr -f traj.xtc -n index.ndx -oaxis helixaxis.dat -ocenter center.dat -orise rise.xvg -oradius radius.xvg -otwist twist.xvg -obending bending.xvg -otilt tilt.xvg -orot rotation.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr -[no]sidechain -[no]incremental DESCRIPTION g_helixorient calculates coordinates and direction of the average…
NAME g_helix – calculates basic properties of alpha helices VERSION 4.0.1 SYNOPSIS g_helix -s topol.tpr -n index.ndx -f traj.xtc -to gtraj.g87 -cz zconf.gro -co waver.gro -[no]h -nice int -b time -e time -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop enum -[no]ev -ahxstart int -ahxend int DESCRIPTION g_helix computes all kind of helix properties….
NAME g_helix – calculates basic properties of alpha helices VERSION 4.0.1 SYNOPSIS g_helix -s topol.tpr -n index.ndx -f traj.xtc -to gtraj.g87 -cz zconf.gro -co waver.gro -[no]h -nice int -b time -e time -dt time -[no]w -r0 int -[no]q -[no]F -[no]db -prop enum -[no]ev -ahxstart int -ahxend int DESCRIPTION g_helix computes all kind of helix properties….
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…