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)