NAME

       g_mdmat - calculates residue contact maps

       VERSION 4.6.5

SYNOPSIS

       g_mdmat  -f  traj.xtc  -s  topol.tpr  -n  index.ndx  -mean  dm.xpm  -frames  dmf.xpm  -no  num.xvg -[no]h
       -[no]version -nice int -b time -e time -dt time -xvg enum -t real -nlevels int

DESCRIPTION

        g_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
       xpm2ps to make a PostScript (tm) plot.

FILES

       -f traj.xtc Input
        Trajectory: xtc trr trj gro g96 pdb cpt

       -s topol.tpr Input
        Structure+mass(db): tpr tpb tpa gro g96 pdb

       -n index.ndx Input, Opt.
        Index file

       -mean dm.xpm Output
        X PixMap compatible matrix file

       -frames dmf.xpm Output, Opt.
        X PixMap compatible matrix file

       -no num.xvg Output, Opt.
        xvgr/xmgr file

OTHER OPTIONS

       -[no]hno
        Print help info and quit

       -[no]versionno
        Print version info and quit

       -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 or  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/>.

                                                 Mon 2 Dec 2013                                       g_mdmat(1)