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       g_mdmat - calculates residue contact maps

       VERSION 4.0.1


       g_mdmat  -f  traj.xtc  -s  topol.tpr  -n index.ndx -mean dm.xpm -frames
       dmf.xpm -no num.xvg -[no]h -nice int -b time -e time -dt time -[no]xvgr
       -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 as a function of time, to be able to see differences in tertiary
       structure as a funcion of time. If you choose your options unwise, this
       may  generate a large output file. 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

       -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)

        Add  specific  codes  (legends  etc.)  in the output xvg files for the
       xmgrace program

       -t real 1.5
        trunc distance

       -nlevels int 40
        Discretize distance in  levels



       More     information     about     GROMACS     is     available      at

                                Thu 16 Oct 2008                     g_mdmat(1)