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gmx-mdmat(1)                    GROMACS Manual                    gmx-mdmat(1)

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)

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

VERSION 5.0.6                                                     gmx-mdmat(1)