g_mindist

NAME

g_mindist - calculates the minimum distance between two groups

VERSION 4.6.6

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 another group with multiple atoms in the first group is counted as one contact instead of as multiple contacts. 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/>.