gmx-mdmat man page

gmx-mdmat — Calculate residue contact maps


gmx mdmat [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
          [-mean [<.xpm>]] [-frames [<.xpm>]] [-no [<.xvg>]]
          [-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 files:

-f [<.xtc/.trr/...>] (traj.xtc)

Trajectory: xtc trr cpt gro g96 pdb tng

-s [<.tpr/.gro/...>] (topol.tpr)

Structure+mass(db): tpr gro g96 pdb brk ent

-n [<.ndx>] (index.ndx) (Optional)

Index file

Options to specify output files:

-mean [<.xpm>] (dm.xpm)

X PixMap compatible matrix file

-frames [<.xpm>] (dmf.xpm) (Optional)

X PixMap compatible matrix file

-no [<.xvg>] (num.xvg) (Optional)

xvgr/xmgr file

Other options:

-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


More information about GROMACS is available at <>.

Referenced By


Mar 13, 2017 2016.3 GROMACS