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.
pdb2gmx – converts pdb files to topology and coordinate files VERSION 4.0.1 Synopsispdb2gmx -f eiwit.pdb -o conf.gro -p topol.top -i posre.itp -n clean.ndx -q clean.pdb -[no]h -nice int -[no]merge -ff string -water enum -[no]inter -[no]ss -[no]ter -[no]lys -[no]arg -[no]asp -[no]glu -[no]gln -[no]his -angle real -dist real -[no]una -[no]ignh -[no]missing -[no]v -posrefc real -vsite enum -[no]heavyh…
pdb2gmx – converts pdb files to topology and coordinate files VERSION 4.0.1 Synopsispdb2gmx -f eiwit.pdb -o conf.gro -p topol.top -i posre.itp -n clean.ndx -q clean.pdb -[no]h -nice int -[no]merge -ff string -water enum -[no]inter -[no]ss -[no]ter -[no]lys -[no]arg -[no]asp -[no]glu -[no]gln -[no]his -angle real -dist real -[no]una -[no]ignh -[no]missing -[no]v -posrefc real -vsite enum -[no]heavyh…
g_order – computes the order parameter per atom for carbon tails VERSION 4.0.1 Synopsisg_order -f traj.xtc -n index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -os sliced.xvg -Sg sg-ang.xvg -Sk sk-dist.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d enum -sl int -[no]szonly -[no]unsat DescriptionCompute the order parameter per atom for carbon…
g_order – computes the order parameter per atom for carbon tails VERSION 4.0.1 Synopsisg_order -f traj.xtc -n index.ndx -s topol.tpr -o order.xvg -od deuter.xvg -os sliced.xvg -Sg sg-ang.xvg -Sk sk-dist.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d enum -sl int -[no]szonly -[no]unsat DescriptionCompute the order parameter per atom for carbon…
g_nmtraj – generate oscillating trajectory of an eigenmode VERSION 4.0.1 Synopsisg_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -nice int -eignr string -phases string -temp real -amplitude real -nframes int Description g_nmtraj generates an virtual trajectory from an eigenvector, corresponding to a harmonic cartesian oscillation around the average structure. The eigenvectors should normally be mass-weighted,…
g_nmtraj – generate oscillating trajectory of an eigenmode VERSION 4.0.1 Synopsisg_nmtraj -s topol.tpr -v eigenvec.trr -o nmtraj.xtc -[no]h -nice int -eignr string -phases string -temp real -amplitude real -nframes int Description g_nmtraj generates an virtual trajectory from an eigenvector, corresponding to a harmonic cartesian oscillation around the average structure. The eigenvectors should normally be mass-weighted,…
g_nmens – generates an ensemble of structures from the normal modes VERSION 4.0.1 Synopsisg_nmens -v eigenvec.trr -e eigenval.xvg -s topol.tpr -n index.ndx -o ensemble.xtc -[no]h -nice int -[no]xvgr -temp real -seed int -num int -first int -last int Description g_nmens generates an ensemble around an average structure in a subspace which is defined by a…
g_nmens – generates an ensemble of structures from the normal modes VERSION 4.0.1 Synopsisg_nmens -v eigenvec.trr -e eigenval.xvg -s topol.tpr -n index.ndx -o ensemble.xtc -[no]h -nice int -[no]xvgr -temp real -seed int -num int -first int -last int Description g_nmens generates an ensemble around an average structure in a subspace which is defined by a…
g_nmeig – diagonalizes the Hessian VERSION 4.0.1 Synopsisg_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 Descriptiong_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 structure is written…
g_nmeig – diagonalizes the Hessian VERSION 4.0.1 Synopsisg_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 Descriptiong_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 structure is written…
ngmx – displays a trajectory VERSION 4.0.1 Synopsisngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -nice int -b time -e time -dt time Descriptionngmx 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 your standard X…
ngmx – displays a trajectory VERSION 4.0.1 Synopsisngmx -f traj.xtc -s topol.tpr -n index.ndx -[no]h -nice int -b time -e time -dt time Descriptionngmx 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 your standard X…
g_msd – calculates mean square displacements VERSION 4.0.1 Synopsisg_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 Descriptiong_msd computes the mean…
g_msd – calculates mean square displacements VERSION 4.0.1 Synopsisg_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 Descriptiong_msd computes the mean…
g_morph – linear interpolation of conformations VERSION 4.0.1 Synopsisg_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 Descriptiong_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to…
g_morph – linear interpolation of conformations VERSION 4.0.1 Synopsisg_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 Descriptiong_morph does a linear interpolation of conformations in order to create intermediates. Of course these are completely unphysical, but that you may try to…
mk_angndx – generates index files for g_angle VERSION 4.0.1 Synopsismk_angndx -s topol.tpr -n angle.ndx -[no]h -nice int -type enum -[no]hyd Descriptionmk_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 input file: tpr tpb…
mk_angndx – generates index files for g_angle VERSION 4.0.1 Synopsismk_angndx -s topol.tpr -n angle.ndx -[no]h -nice int -type enum -[no]hyd Descriptionmk_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 input file: tpr tpb…
g_mindist – calculates the minimum distance between two groups VERSION 4.0.1 Synopsisg_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 Descriptiong_mindist computes the distance between…
g_mindist – calculates the minimum distance between two groups VERSION 4.0.1 Synopsisg_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 Descriptiong_mindist computes the distance between…