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# gmx-mindist - Calculate the minimum distance between two groups

 GMX-MINDIST(1) GROMACS GMX-MINDIST(1)

## NAME

gmx-mindist - Calculate the minimum distance between two groups

## SYNOPSIS

```gmx mindist [ -f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
[ -od [<.xvg>]] [-on [<.xvg>]] [-o [<.out>]]
[ -ox [<.xtc/.trr/...>]] [-or [<.xvg>]] [-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

gmx 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.

Also gmx distance and gmx pairdist calculate distances.

## OPTIONS

Options to specify input files:
-f [<.xtc/.trr/...>] (traj.xtc)
Trajectory: xtc trr cpt gro g96 pdb tng
-s [<.tpr/.gro/...>] (topol.tpr) (Optional)
Structure+mass(db): tpr gro g96 pdb brk ent
-n [<.ndx>] (index.ndx) (Optional)
Index file

Options to specify output files:
-od [<.xvg>] (mindist.xvg)
xvgr/xmgr file
-on [<.xvg>] (numcont.xvg) (Optional)
xvgr/xmgr file
-o [<.out>] (atm-pair.out) (Optional)
Generic output file
-ox [<.xtc/.trr/...>] (mindist.xtc) (Optional)
Trajectory: xtc trr gro g96 pdb tng
-or [<.xvg>] (mindistres.xvg) (Optional)
xvgr/xmgr file

Other options:
-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)
Unit for time values: fs, ps, ns, us, ms, s
-[no]w (no)
View output .xvg, .xpm, .eps and .pdb files
-xvg <enum> (xmgrace)
xvg plot formatting: xmgrace, xmgr, none
-[no]matrix (no)
Calculate half a matrix of group-group distances
-[no]max (no)
Calculate maximum distance instead of minimum
-d <real> (0.6)
Distance for contacts
-[no]group (no)
Count contacts with multiple atoms in the first group as one
-[no]pi (no)
Calculate minimum distance with periodic images
-[no]split (no)
Split graph where time is zero
-ng <int> (1)
Number of secondary groups to compute distance to a central group
-[no]pbc (yes)
Take periodic boundary conditions into account
-[no]respertime (no)
When writing per-residue distances, write distance for each time point
-[no]printresname (no)
Write residue names