.. _gmx confrms:

gmx confrms
===========

Synopsis
--------

.. parsed-literal::

    gmx confrms [:strong:`-f1` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-f2` :emphasis:`[<.gro/.g96/...>]`]
                [:strong:`-n1` :emphasis:`[<.ndx>]`] [:strong:`-n2` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.gro/.g96/...>]`]
                [:strong:`-no` :emphasis:`[<.ndx>]`] [:strong:`-[no]w`] [:strong:`-[no]one`] [:strong:`-[no]mw`] [:strong:`-[no]pbc`]
                [:strong:`-[no]fit`] [:strong:`-[no]name`] [:strong:`-[no]label`] [:strong:`-[no]bfac`]

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

``gmx confrms`` computes the root mean square deviation (RMSD) of two
structures after least-squares fitting the second structure on the first one.
The two structures do NOT need to have the same number of atoms,
only the two index groups used for the fit need to be identical.
With ``-name`` only matching atom names from the selected groups
will be used for the fit and RMSD calculation. This can be useful
when comparing mutants of a protein.

The superimposed structures are written to file. In a :ref:`.pdb <pdb>` file
the two structures will be written as separate models
(use ``rasmol -nmrpdb``). Also in a :ref:`.pdb <pdb>` file, B-factors
calculated from the atomic MSD values can be written with ``-bfac``.

Options
-------

Options to specify input files:

``-f1`` [<.tpr/.gro/...>] (conf1.gro)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-f2`` [<.gro/.g96/...>] (conf2.gro)
    Structure file: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`tpr`
``-n1`` [<.ndx>] (fit1.ndx) (Optional)
    Index file
``-n2`` [<.ndx>] (fit2.ndx) (Optional)
    Index file

Options to specify output files:

``-o`` [<.gro/.g96/...>] (fit.pdb)
    Structure file: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp
``-no`` [<.ndx>] (match.ndx) (Optional)
    Index file

Other options:

``-[no]w``  (no)
    View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <pdb>` files
``-[no]one``  (no)
    Only write the fitted structure to file
``-[no]mw``  (yes)
    Mass-weighted fitting and RMSD
``-[no]pbc``  (no)
    Try to make molecules whole again
``-[no]fit``  (yes)
    Do least squares superposition of the target structure to the reference
``-[no]name``  (no)
    Only compare matching atom names
``-[no]label``  (no)
    Added chain labels A for first and B for second structure
``-[no]bfac``  (no)
    Output B-factors from atomic MSD values

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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