.. _gmx mdmat:

gmx mdmat
=========

Synopsis
--------

.. parsed-literal::

    gmx mdmat [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
              [:strong:`-mean` :emphasis:`[<.xpm>]`] [:strong:`-frames` :emphasis:`[<.xpm>]`] [:strong:`-no` :emphasis:`[<.xvg>]`]
              [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-xvg` :emphasis:`<enum>`]
              [:strong:`-t` :emphasis:`<real>`] [:strong:`-nlevels` :emphasis:`<int>`]

Description
-----------

``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 :doc:`gmx xpm2ps <gmx-xpm2ps>` to make a PostScript (tm) plot.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`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)
    Time of first frame to read from trajectory (default unit ps)
``-e`` <time> (0)
    Time of last frame to read from trajectory (default unit ps)
``-dt`` <time> (0)
    Only use frame when t MOD dt = first time (default unit 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

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

   More information about |Gromacs| is available at <http://www.gromacs.org/>.