.. _gmx rmsdist:

gmx rmsdist
===========
Synopsis
--------
.. parsed-literal::

    gmx rmsdist [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                [:strong:`-equiv` :emphasis:`[<.dat>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-rms` :emphasis:`[<.xpm>]`]
                [:strong:`-scl` :emphasis:`[<.xpm>]`] [:strong:`-mean` :emphasis:`[<.xpm>]`] [:strong:`-nmr3` :emphasis:`[<.xpm>]`]
                [:strong:`-nmr6` :emphasis:`[<.xpm>]`] [:strong:`-noe` :emphasis:`[<.dat>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
                [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-nlevels` :emphasis:`<int>`]
                [:strong:`-max` :emphasis:`<real>`] [:strong:`-[no]sumh`] [:strong:`-[no]pbc`]

Description
-----------
``gmx rmsdist`` computes the root mean square deviation of atom distances,
which has the advantage that no fit is needed like in standard RMS
deviation as computed by :doc:`gmx rms <gmx-rms>`.
The reference structure is taken from the structure file.
The RMSD at time t is calculated as the RMS
of the differences in distance between atom-pairs in the reference
structure and the structure at time t.

``gmx rmsdist`` can also produce matrices of the rms distances, rms distances
scaled with the mean distance and the mean distances and matrices with
NMR averaged distances (1/r^3 and 1/r^6 averaging). Finally, lists
of atom pairs with 1/r^3 and 1/r^6 averaged distance below the
maximum distance (``-max``, which will default to 0.6 in this case)
can be generated, by default averaging over equivalent hydrogens
(all triplets of hydrogens named \*[123]). Additionally a list of
equivalent atoms can be supplied (``-equiv``), each line containing
a set of equivalent atoms specified as residue number and name and
atom name; e.g.:

``HB* 3 SER  HB1 3 SER  HB2``

Residue and atom names must exactly match those in the structure
file, including case. Specifying non-sequential atoms is undefined.

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
``-equiv`` [<.dat>] (equiv.dat) (Optional)
    Generic data file

Options to specify output files:

``-o`` [<.xvg>] (distrmsd.xvg)
    xvgr/xmgr file
``-rms`` [<.xpm>] (rmsdist.xpm) (Optional)
    X PixMap compatible matrix file
``-scl`` [<.xpm>] (rmsscale.xpm) (Optional)
    X PixMap compatible matrix file
``-mean`` [<.xpm>] (rmsmean.xpm) (Optional)
    X PixMap compatible matrix file
``-nmr3`` [<.xpm>] (nmr3.xpm) (Optional)
    X PixMap compatible matrix file
``-nmr6`` [<.xpm>] (nmr6.xpm) (Optional)
    X PixMap compatible matrix file
``-noe`` [<.dat>] (noe.dat) (Optional)
    Generic data 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)
``-[no]w``  (no)
    View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <pdb>` files
``-xvg`` <enum>
    xvg plot formatting: xmgrace, xmgr, none
``-nlevels`` <int> (40)
    Discretize RMS in this number of levels
``-max`` <real> (-1)
    Maximum level in matrices
``-[no]sumh``  (yes)
    Average distance over equivalent hydrogens
``-[no]pbc``  (yes)
    Use periodic boundary conditions when computing distances


.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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