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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)

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


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