.TH gmx-mdmat 1 "" "VERSION 5.0.2" "GROMACS Manual"
.SH NAME
gmx-mdmat \- Calculate residue contact maps

.SH 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>]

.SH DESCRIPTION
\fBgmx mdmat\fR makes distance matrices consisting of the smallest distance between residue pairs. With \fB\-frames\fR, 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 \fBgmx xpm2ps\fR to make a PostScript (tm) plot.

.SH OPTIONS
Options to specify input and output files:

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

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

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

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

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

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


Other options:

.BI "\-nice" " <int> (19)"
    Set the nicelevel

.BI "\-b" " <time> (0)"
    First frame (ps) to read from trajectory

.BI "\-e" " <time> (0)"
    Last frame (ps) to read from trajectory

.BI "\-dt" " <time> (0)"
    Only use frame when t MOD dt = first time (ps)

.BI "\-xvg" " <enum> (xmgrace)"
    xvg plot formatting: xmgrace, xmgr, none

.BI "\-t" " <real> (1.5)"
    trunc distance

.BI "\-nlevels" " <int> (40)"
    Discretize distance in this number of levels


.SH SEE ALSO
.BR gromacs(7)

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