GMX-MDMAT(1) GROMACS GMX-MDMAT(1) 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 be- tween 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 h5md -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) More information about GROMACS is available at <http://www.gromacs.org/>. COPYRIGHT 2026, GROMACS development team 2026.3 Jun 25, 2026 GMX-MDMAT(1)
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