---
name: "g_mdmat_d"
section: "1"
platform: "linux"
package: "gromacs-data"
version: "5.0.2-1"
release: "Debian 8 (Jessie)"
platforms: ["linux"]
url: "https://new.carta.tech/gmx-mdmat"
---

# g\_mdmat\_d(1)

Calculate residue contact maps

Part of [gmx-mdmat(1)](/gmx-mdmat/1.md).

## NAME

gmx-mdmat - Calculate residue contact maps

## SYNOPSIS

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

## 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 and output files:

**-f** *\[\<.xtc/.trr/...\>\] (traj.xtc) (Input)*\
     Trajectory: xtc trr cpt trj gro g96 pdb tng

**-s** *\[\<.tpr/.tpb/...\>\] (topol.tpr) (Input)*\
     Structure+mass(db): tpr tpb tpa gro g96 pdb brk ent

**-n** *\[\<.ndx\>\] (index.ndx) (Input, Optional)*\
     Index file

**-mean** *\[\<.xpm\>\] (dm.xpm) (Output)*\
     X PixMap compatible matrix file

**-frames** *\[\<.xpm\>\] (dmf.xpm) (Output, Optional)*\
     X PixMap compatible matrix file

**-no** *\[\<.xvg\>\] (num.xvg) (Output, Optional)*\
     xvgr/xmgr file

Other options:

**-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)

**-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

**[gromacs(7)](/gromacs/7.md)**

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