.. _gmx saxs:

gmx saxs
========

Synopsis
--------

.. parsed-literal::

    gmx saxs [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
             [:strong:`-d` :emphasis:`[<.dat>]`] [:strong:`-sq` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
             [:strong:`-dt` :emphasis:`<time>`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-ng` :emphasis:`<int>`] [:strong:`-startq` :emphasis:`<real>`]
             [:strong:`-endq` :emphasis:`<real>`] [:strong:`-energy` :emphasis:`<real>`]

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

``gmx saxs`` calculates SAXS structure factors for given index
groups based on Cromer's method.
Both topology and trajectory files are required.

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

Options to specify output files:

``-sq`` [<.xvg>] (sq.xvg)
    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
``-ng`` <int> (1)
    Number of groups to compute SAXS
``-startq`` <real> (0)
    Starting q (1/nm)
``-endq`` <real> (60)
    Ending q (1/nm)
``-energy`` <real> (12)
    Energy of the incoming X-ray (keV)

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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