---
name: "gmx-mindist"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "2025.2-1"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-mindist"
---

# gmx-mindist(1)

Calculate the minimum distance between two groups

## 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. Note that periodicity information is required from the file supplied with with **-s**, either as a .tpr file or a .pdb file with CRYST1 fields. 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)**

  Time of first frame to read from trajectory (default unit ps)

- **-e \<time\> (0)**

  Time of last frame to read from trajectory (default unit ps)

- **-dt \<time\> (0)**

  Only use frame when t MOD dt = first time (default unit 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

## SEE ALSO

**[gmx(1)](/gmx/1.md)**

More information about GROMACS is available at \<*http://www.gromacs.org/*\>.

## COPYRIGHT

2025, GROMACS development team