Provided by: gromacs-data_4.6.5-1build1_all bug


       g_mdmat - calculates residue contact maps

       VERSION 4.6.5


       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


        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.


       -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


        Print help info and quit

        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



       More information about GROMACS is available at <>.

                                          Mon 2 Dec 2013                               g_mdmat(1)