g_mdmat_d (1)

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>]

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 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

gromacs(7)

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