g_rama – computes Ramachandran plots VERSION 4.0.1 Synopsisg_rama -f traj.xtc -s topol.tpr -o rama.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr Descriptiong_rama selects the Phi/Psi dihedral combinations from your topology file and computes these as a function of time. Using simple Unix tools such as grep you can select out specific…
protonate – protonates structures VERSION 4.0.1 Synopsisprotonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time Description protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb. If only -s is specified, this conformation will be protonated, if also -f is specified, the conformation(s)…
protonate – protonates structures VERSION 4.0.1 Synopsisprotonate -s topol.tpr -f traj.xtc -n index.ndx -o protonated.xtc -[no]h -nice int -b time -e time -dt time Description protonate reads (a) conformation(s) and adds all missing hydrogens as defined in ffgmx2.hdb. If only -s is specified, this conformation will be protonated, if also -f is specified, the conformation(s)…
g_principal – calculates axes of inertia for a group of atoms VERSION 4.0.1 Synopsisg_principal -f traj.xtc -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]foo Descriptiong_principal calculates the three principal axes of inertia for a group of atoms. Files-f…
g_principal – calculates axes of inertia for a group of atoms VERSION 4.0.1 Synopsisg_principal -f traj.xtc -s topol.tpr -n index.ndx -a1 axis1.dat -a2 axis2.dat -a3 axis3.dat -om moi.dat -[no]h -nice int -b time -e time -dt time -tu enum -[no]w -[no]foo Descriptiong_principal calculates the three principal axes of inertia for a group of atoms. Files-f…
g_potential – calculates the electrostatic potential across the box VERSION 4.0.1 Synopsisg_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correct DescriptionCompute the electrostatical potential across the…
g_potential – calculates the electrostatic potential across the box VERSION 4.0.1 Synopsisg_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -nice int -b time -e time -dt time -[no]w -[no]xvgr -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correct DescriptionCompute the electrostatical potential across the…
g_polystat – calculates static properties of polymers VERSION 4.0.1 Synopsisg_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 Descriptiong_polystat plots static properties of polymers as a function of time and prints the average. By default it…
g_polystat – calculates static properties of polymers VERSION 4.0.1 Synopsisg_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 Descriptiong_polystat plots static properties of polymers as a function of time and prints the average. By default it…
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…