.. _gmx sans:

gmx sans
========

Synopsis
--------

.. parsed-literal::

    gmx sans [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
             [:strong:`-d` :emphasis:`[<.dat>]`] [:strong:`-pr` :emphasis:`[<.xvg>]`] [:strong:`-sq` :emphasis:`[<.xvg>]`]
             [:strong:`-prframe` :emphasis:`[<.xvg>]`] [:strong:`-sqframe` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`]
             [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-xvg` :emphasis:`<enum>`]
             [:strong:`-bin` :emphasis:`<real>`] [:strong:`-mode` :emphasis:`<enum>`] [:strong:`-mcover` :emphasis:`<real>`]
             [:strong:`-method` :emphasis:`<enum>`] [:strong:`-[no]pbc`] [:strong:`-grid` :emphasis:`<real>`] [:strong:`-startq` :emphasis:`<real>`]
             [:strong:`-endq` :emphasis:`<real>`] [:strong:`-qstep` :emphasis:`<real>`] [:strong:`-seed` :emphasis:`<int>`] [:strong:`-nt` :emphasis:`<int>`]

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

``gmx sans`` computes SANS spectra using Debye formula.
It currently uses topology file (since it need to assigne element for each atom).

Parameters:

``-pr`` Computes normalized g(r) function averaged over trajectory

``-prframe`` Computes normalized g(r) function for each frame

``-sq`` Computes SANS intensity curve averaged over trajectory

``-sqframe`` Computes SANS intensity curve for each frame

``-startq`` Starting q value in nm

``-endq`` Ending q value in nm

``-qstep`` Stepping in q space

Note: When using Debye direct method computational cost increases as
1/2 * N * (N - 1) where N is atom number in group of interest.

WARNING: If sq or pr specified this tool can produce large number of files! Up to
two times larger than number of frames!

Options
-------

Options to specify input files:

``-s`` [<.tpr>] (topol.tpr)
    Portable xdr run input file
``-f`` [<.xtc/.trr/...>] (traj.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file
``-d`` [<.dat>] (nsfactor.dat) (Optional)
    Generic data file

Options to specify output files:

``-pr`` [<.xvg>] (pr.xvg)
    xvgr/xmgr file
``-sq`` [<.xvg>] (sq.xvg)
    xvgr/xmgr file
``-prframe`` [<.xvg>] (prframe.xvg) (Optional)
    xvgr/xmgr file
``-sqframe`` [<.xvg>] (sqframe.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)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-bin`` <real> (0.2)
    [HIDDEN]Binwidth (nm)
``-mode`` <enum> (direct)
    Mode for sans spectra calculation: direct, mc
``-mcover`` <real> (-1)
    Monte-Carlo coverage should be -1(default) or (0,1]
``-method`` <enum> (debye)
    [HIDDEN]Method for sans spectra calculation: debye, fft
``-[no]pbc``  (yes)
    Use periodic boundary conditions for computing distances
``-grid`` <real> (0.05)
    [HIDDEN]Grid spacing (in nm) for FFTs
``-startq`` <real> (0)
    Starting q (1/nm)
``-endq`` <real> (2)
    Ending q (1/nm)
``-qstep`` <real> (0.01)
    Stepping in q (1/nm)
``-seed`` <int> (0)
    Random seed for Monte-Carlo
``-nt`` <int> (64)
    Number of threads to start

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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