Section 1: user commands and tools
NAME g_polystat – calculates static properties of polymers VERSION 4.0.1 SYNOPSIS g_polystat -s topol.tpr -f traj.xtc -n index.ndx -o polystat.xvg -v polyvec.xvg -p persist.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]mw -[no]pc DESCRIPTION g_polystat plots static properties of polymers as a function of time and prints the average….
NAME g_polystat – calculates static properties of polymers VERSION 4.0.1 SYNOPSIS g_polystat -s topol.tpr -f traj.xtc -n index.ndx -o polystat.xvg -v polyvec.xvg -p persist.xvg -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]xvgr -[no]mw -[no]pc DESCRIPTION g_polystat plots static properties of polymers as a function of time and prints the average….
NAME pdb2gmx – converts pdb files to topology and coordinate files VERSION 4.0.1 SYNOPSIS pdb2gmx -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…
NAME pdb2gmx – converts pdb files to topology and coordinate files VERSION 4.0.1 SYNOPSIS pdb2gmx -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…
NAME g_order – computes the order parameter per atom for carbon tails VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION Compute the order parameter per…
NAME g_order – computes the order parameter per atom for carbon tails VERSION 4.0.1 SYNOPSIS g_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 DESCRIPTION Compute the order parameter per…
NAME g_nmtraj – generate oscillating trajectory of an eigenmode VERSION 4.0.1 SYNOPSIS g_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…
NAME g_nmtraj – generate oscillating trajectory of an eigenmode VERSION 4.0.1 SYNOPSIS g_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…
NAME g_nmens – generates an ensemble of structures from the normal modes VERSION 4.0.1 SYNOPSIS g_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…
NAME g_nmens – generates an ensemble of structures from the normal modes VERSION 4.0.1 SYNOPSIS g_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…
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 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…