.. _gmx saltbr:

gmx saltbr
==========

Synopsis
--------

.. parsed-literal::

    gmx saltbr [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
               [:strong:`-dt` :emphasis:`<time>`] [:strong:`-t` :emphasis:`<real>`] [:strong:`-[no]sep`]

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

``gmx saltbr`` plots the distance between all combination of charged groups
as a function of time. The groups are combined in different ways.
A minimum distance can be given (i.e. a cut-off), such that groups
that are never closer than that distance will not be plotted.

Output will be in a number of fixed filenames, ``min-min.xvg``, ``plus-min.xvg``
and ``plus-plus.xvg``, or files for every individual ion pair if the ``-sep``
option is selected. In this case, files are named as
``sb-(Resname)(Resnr)-(Atomnr)``.
There may be **many** such files.

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>] (topol.tpr)
    Portable xdr run input 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)
``-t`` <real> (1000)
    Groups that are never closer than this distance are not plotted
``-[no]sep``  (no)
    Use separate files for each interaction (may be MANY)

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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