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 g_nmeig – diagonalizes the Hessian VERSION 4.0.1 SYNOPSIS g_nmeig -f hessian.mtx -s topol.tpr -of eigenfreq.xvg -ol eigenval.xvg -v eigenvec.trr -[no]h -nice int -[no]xvgr -[no]m -first int -last int DESCRIPTION g_nmeig calculates the eigenvectors/values of a (Hessian) matrix, which can be calculated with mdrun. The eigenvectors are written to a trajectory file ( -v). The…
NAME ngmx – displays a trajectory VERSION 4.0.1 SYNOPSIS ngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -nice int -b time -e time -dt time DESCRIPTION ngmx is the Gromacs trajectory viewer. This program reads a trajectory file, a run input file and an index file and plots a 3D structure of your molecule on…
NAME ngmx – displays a trajectory VERSION 4.0.1 SYNOPSIS ngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -nice int -b time -e time -dt time DESCRIPTION ngmx is the Gromacs trajectory viewer. This program reads a trajectory file, a run input file and an index file and plots a 3D structure of your molecule on…
NAME g_msd – calculates mean square displacements VERSION 4.0.1 SYNOPSIS g_msd -f traj.xtc -s topol.tpr -n index.ndx -o msd.xvg -mol diff_mol.xvg -pdb diff_mol.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -type enum -lateral enum -[no]ten -ngroup int -[no]mw -[no]rmcomm -tpdb time -trestart time -beginfit time -endfit time DESCRIPTION g_msd…
NAME g_msd – calculates mean square displacements VERSION 4.0.1 SYNOPSIS g_msd -f traj.xtc -s topol.tpr -n index.ndx -o msd.xvg -mol diff_mol.xvg -pdb diff_mol.pdb -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -type enum -lateral enum -[no]ten -ngroup int -[no]mw -[no]rmcomm -tpdb time -trestart time -beginfit time -endfit time DESCRIPTION g_msd…
NAME g_morph – linear interpolation of conformations VERSION 4.0.1 SYNOPSIS g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -nice int -[no]w -[no]xvgr -ninterm int -first real -last real -[no]fit DESCRIPTION g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you…
NAME g_morph – linear interpolation of conformations VERSION 4.0.1 SYNOPSIS g_morph -f1 conf1.gro -f2 conf2.gro -o interm.xtc -or rms-interm.xvg -n index.ndx -[no]h -nice int -[no]w -[no]xvgr -ninterm int -first real -last real -[no]fit DESCRIPTION g_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you…
NAME mk_angndx – generates index files for g_angle VERSION 4.0.1 SYNOPSIS mk_angndx -s topol.tpr -n angle.ndx -[no]h -nice int -type enum -[no]hyd DESCRIPTION mk_angndx makes an index file for calculation of angle distributions etc. It uses a run input file ( .tpx) for the definitions of the angles, dihedrals etc. FILES -s topol.tpr Input Run…
NAME mk_angndx – generates index files for g_angle VERSION 4.0.1 SYNOPSIS mk_angndx -s topol.tpr -n angle.ndx -[no]h -nice int -type enum -[no]hyd DESCRIPTION mk_angndx makes an index file for calculation of angle distributions etc. It uses a run input file ( .tpx) for the definitions of the angles, dihedrals etc. FILES -s topol.tpr Input Run…
NAME g_mindist – calculates the minimum distance between two groups VERSION 4.0.1 SYNOPSIS g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]matrix -[no]max -d real -[no]pi -[no]split -ng int -[no]pbc DESCRIPTION g_mindist computes…
NAME g_mindist – calculates the minimum distance between two groups VERSION 4.0.1 SYNOPSIS g_mindist -f traj.xtc -s topol.tpr -n index.ndx -od mindist.xvg -on numcont.xvg -o atm-pair.out -ox mindist.xtc -or mindistres.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]matrix -[no]max -d real -[no]pi -[no]split -ng int -[no]pbc DESCRIPTION g_mindist computes…
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 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…