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

# gmx-mdmat(1)

Calculate residue contact maps

## NAME

gmx-mdmat - Calculate residue contact maps

## SYNOPSIS

```
gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
          [-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
          [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
          [-t <real>] [-nlevels <int>]
```

## DESCRIPTION

**gmx mdmat** makes distance matrices consisting of the smallest distance between residue pairs. With **-frames**, these distance matrices can be stored in order to see differences in tertiary structure as a function of time. If you choose your options unwisely, this may generate a large output file. By default, only an averaged matrix over the whole trajectory is output. Also a count of the number of different atomic contacts between residues over the whole trajectory can be made. The output can be processed with *gmx xpm2ps* to make a PostScript (tm) plot.

## OPTIONS

Options to specify input files:

- **-f \[\<.xtc/.trr/...\>\] (traj.xtc)**

  Trajectory: *xtc* *trr* *cpt* *gro* *g96* *pdb* *tng*

- **-s \[\<.tpr/.gro/...\>\] (topol.tpr)**

  Structure+mass(db): *tpr* *gro* *g96* *pdb* brk ent

- **-n \[\<.ndx\>\] (index.ndx) (Optional)**

  Index file

Options to specify output files:

- **-mean \[\<.xpm\>\] (dm.xpm)**

  X PixMap compatible matrix file

- **-frames \[\<.xpm\>\] (dmf.xpm) (Optional)**

  X PixMap compatible matrix file

- **-no \[\<.xvg\>\] (num.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)

- **-xvg \<enum\> (xmgrace)**

  xvg plot formatting: xmgrace, xmgr, none

- **-t \<real\> (1.5)**

  trunc distance

- **-nlevels \<int\> (40)**

  Discretize distance in this number of levels

## SEE ALSO

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

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

## COPYRIGHT

2025, GROMACS development team