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 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/>.