.. _gmx rmsf:

gmx rmsf
========

Synopsis
--------

.. parsed-literal::

    gmx rmsf [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
             [:strong:`-q` :emphasis:`[<.pdb>]`] [:strong:`-oq` :emphasis:`[<.pdb>]`] [:strong:`-ox` :emphasis:`[<.pdb>]`] [:strong:`-o` :emphasis:`[<.xvg>]`]
             [:strong:`-od` :emphasis:`[<.xvg>]`] [:strong:`-oc` :emphasis:`[<.xvg>]`] [:strong:`-dir` :emphasis:`[<.log>]`] [:strong:`-b` :emphasis:`<time>`]
             [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]res`]
             [:strong:`-[no]aniso`] [:strong:`-[no]fit`]

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

``gmx rmsf`` computes the root mean square fluctuation (RMSF, i.e. standard
deviation) of atomic positions in the trajectory (supplied with ``-f``)
after (optionally) fitting to a reference frame (supplied with ``-s``).

With option ``-oq`` the RMSF values are converted to B-factor
values, which are written to a :ref:`.pdb <pdb>` file. By default, the coordinates
in this output file are taken from the structure file provided with ``-s``,although you can also use coordinates read from a different :ref:`.pdb <pdb>` fileprovided with ``-q``. There is very little error checking, so in this caseit is your responsibility to make sure all atoms in the structure fileand :ref:`.pdb <pdb>` file correspond exactly to each other.

Option ``-ox`` writes the B-factors to a file with the average
coordinates in the trajectory.

With the option ``-od`` the root mean square deviation with
respect to the reference structure is calculated.

With the option ``-aniso``, ``gmx rmsf`` will compute anisotropic
temperature factors and then it will also output average coordinates
and a :ref:`.pdb <pdb>` file with ANISOU records (corresonding to the ``-oq``
or ``-ox`` option). Please note that the U values
are orientation-dependent, so before comparison with experimental data
you should verify that you fit to the experimental coordinates.

When a :ref:`.pdb <pdb>` input file is passed to the program and the ``-aniso``
flag is set
a correlation plot of the Uij will be created, if any anisotropic
temperature factors are present in the :ref:`.pdb <pdb>` file.

With option ``-dir`` the average MSF (3x3) matrix is diagonalized.
This shows the directions in which the atoms fluctuate the most and
the least.

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
``-q`` [<.pdb>] (eiwit.pdb) (Optional)
    Protein data bank file

Options to specify output files:

``-oq`` [<.pdb>] (bfac.pdb) (Optional)
    Protein data bank file
``-ox`` [<.pdb>] (xaver.pdb) (Optional)
    Protein data bank file
``-o`` [<.xvg>] (rmsf.xvg)
    xvgr/xmgr file
``-od`` [<.xvg>] (rmsdev.xvg) (Optional)
    xvgr/xmgr file
``-oc`` [<.xvg>] (correl.xvg) (Optional)
    xvgr/xmgr file
``-dir`` [<.log>] (rmsf.log) (Optional)
    Log 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)
``-[no]w``  (no)
    View output :ref:`.xvg <xvg>`, :ref:`.xpm <xpm>`, :ref:`.eps <eps>` and :ref:`.pdb <pdb>` files
``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-[no]res``  (no)
    Calculate averages for each residue
``-[no]aniso``  (no)
    Compute anisotropic termperature factors
``-[no]fit``  (yes)
    Do a least squares superposition before computing RMSF. Without this you must make sure that the reference structure and the trajectory match.

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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