.. _gmx scattering:

gmx scattering
==============

Synopsis
--------

.. parsed-literal::

    gmx scattering [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`]
                 [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
                 [:strong:`-dt` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-fgroup` :emphasis:`<selection>`]
                 [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]rmpbc`] [:strong:`-[no]pbc`] [:strong:`-sf` :emphasis:`<file>`]
                 [:strong:`-selrpos` :emphasis:`<enum>`] [:strong:`-seltype` :emphasis:`<enum>`] [:strong:`-sel` :emphasis:`<selection>`]
                 [:strong:`-startq` :emphasis:`<real>`] [:strong:`-endq` :emphasis:`<real>`] [:strong:`-qspacing` :emphasis:`<real>`]
                 [:strong:`-binwidth` :emphasis:`<real>`] [:strong:`-mc-coverage` :emphasis:`<real>`] [:strong:`-seed` :emphasis:`<int>`]
                 [:strong:`-[no]norm`] [:strong:`-[no]mc`] [:strong:`-scattering-type` :emphasis:`<enum>`]

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

``gmx scattering`` calculates SANS and SAXS scattering curves using Debye method.

The scattering intensity, I(q), as a function of scattering angle q
with averaging over frames.

Note that this is a new implementation of the SANS/SAXS utilities added in
GROMACS 2024. If you need the old ones,
use ``gmx sans-legacy`` or ``gmx saxs-legacy``.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Input trajectory or single configuration: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Input structure: :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Extra index groups

Options to specify output files:

``-o`` [<.xvg>] (scattering.xvg) (Optional)
    scattering intensity as a function of q

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 if t MOD dt == first time (ps)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-fgroup`` <selection>
    Atoms stored in the trajectory file (if not set, assume first N atoms)
``-xvg`` <enum> (xmgrace)
    Plot formatting: xmgrace, xmgr, none
``-[no]rmpbc``  (yes)
    Make molecules whole for each frame
``-[no]pbc``  (yes)
    Use periodic boundary conditions for distance calculation
``-sf`` <file>
    Provide selections from files
``-selrpos`` <enum> (atom)
    Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-seltype`` <enum> (atom)
    Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-sel`` <selection>
    Selection for Scattering calculation
``-startq`` <real> (0)
    smallest q value (1/nm)
``-endq`` <real> (2)
    largest q value (1/nm)
``-qspacing`` <real> (0.01)
    spacing of q values (1/nm)
``-binwidth`` <real> (0.1)
    Bin width (nm) for P(r)
``-mc-coverage`` <real> (0.2)
    coverage of Monte Carlo (%)
``-seed`` <int> (2023)
    random seed for Monte Carlo
``-[no]norm``  (no)
    normalize scattering intensities
``-[no]mc``  (yes)
    use Monte Carlo to scattering intensities
``-scattering-type`` <enum> (sans)
    Scattering type: saxs, sans

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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