g_potential(1) [debian man page]
g_potential(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_potential(1) NAME
g_potential - calculates the electrostatic potential across the box VERSION 4.5.4-dev-20110404-bc5695c SYNOPSIS
g_potential -f traj.xtc -n index.ndx -s topol.tpr -o potential.xvg -oc charge.xvg -of field.xvg -[no]h -[no]version -nice int -b time -e time -dt time -[no]w -xvg enum -d string -sl int -cb int -ce int -tz real -[no]spherical -ng int -[no]correct DESCRIPTION
g_potential computes the electrostatical potential across the box. The potential is calculated by first summing the charges per slice and then integrating twice of this charge distribution. Periodic boundaries are not taken into account. Reference of potential is taken to be the left side of the box. It is also possible to calculate the potential in spherical coordinates as function of r by calculating a charge distribution in spherical slices and twice integrating them. epsilon_r is taken as 1, but 2 is more appropriate in many cases. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -n index.ndx Input Index file -s topol.tpr Input Run input file: tpr tpb tpa -o potential.xvg Output xvgr/xmgr file -oc charge.xvg Output xvgr/xmgr file -of field.xvg Output xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -d string Z Take the normal on the membrane in direction X, Y or Z. -sl int 10 Calculate potential as function of boxlength, dividing the box in nr slices. -cb int 0 Discard first nr slices of box for integration -ce int 0 Discard last nr slices of box for integration -tz real 0 Translate all coordinates distance in the direction of the box -[no]sphericalno Calculate spherical thingie -ng int 1 Number of groups to consider -[no]correctno Assume net zero charge of groups to improve accuracy KNOWN PROBLEMS
- Discarding slices for integration should not be necessary. SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_potential(1)
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g_mindist(1) GROMACS suite, VERSION 4.5.4-dev-20110404-bc5695c g_mindist(1) NAME
g_mindist - calculates the minimum distance between two groups VERSION 4.5.4-dev-20110404-bc5695c 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 -[no]version -nice int -b time -e time -dt time -tu enum -[no]w -xvg enum -[no]matrix -[no]max -d real -[no]group -[no]pi -[no]split -ng int -[no]pbc -[no]respertime -[no]printresname DESCRIPTION
g_mindist computes the distance between one group and a number of other groups. Both the minimum distance (between any pair of atoms from the respective groups) and the number of contacts within a given distance are written to two separate output files. With the -group option a contact of an atom in other group with multiple atoms in the first group is counted as one contact instead of as multiple con- tacts. With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number. With option -pi the minimum distance of a group to its periodic image is plotted. This is useful for checking if a protein has seen its periodic image during a simulation. Only one shift in each direction is considered, giving a total of 26 shifts. It also plots the maximum distance within the group and the lengths of the three box vectors. Other programs that calculate distances are g_dist and g_bond. FILES
-f traj.xtc Input Trajectory: xtc trr trj gro g96 pdb cpt -s topol.tpr Input, Opt. Structure+mass(db): tpr tpb tpa gro g96 pdb -n index.ndx Input, Opt. Index file -od mindist.xvg Output xvgr/xmgr file -on numcont.xvg Output, Opt. xvgr/xmgr file -o atm-pair.out Output, Opt. Generic output file -ox mindist.xtc Output, Opt. Trajectory: xtc trr trj gro g96 pdb -or mindistres.xvg Output, Opt. xvgr/xmgr file OTHER OPTIONS
-[no]hno Print help info and quit -[no]versionno Print version info and quit -nice int 19 Set the nicelevel -b time 0 First frame (ps) to read from trajectory -e time 0 Last frame (ps) to read from trajectory -dt time 0 Only use frame when t MOD dt = first time (ps) -tu enum ps Time unit: fs, ps, ns, us, ms or s -[no]wno View output .xvg, .xpm, .eps and .pdb files -xvg enum xmgrace xvg plot formatting: xmgrace, xmgr or none -[no]matrixno Calculate half a matrix of group-group distances -[no]maxno Calculate *maximum* distance instead of minimum -d real 0.6 Distance for contacts -[no]groupno Count contacts with multiple atoms in the first group as one -[no]pino Calculate minimum distance with periodic images -[no]splitno Split graph where time is zero -ng int 1 Number of secondary groups to compute distance to a central group -[no]pbcyes Take periodic boundary conditions into account -[no]respertimeno When writing per-residue distances, write distance for each time point -[no]printresnameno Write residue names SEE ALSO
gromacs(7) More information about GROMACS is available at <http://www.gromacs.org/>. Mon 4 Apr 2011 g_mindist(1)