.. _gmx sorient:

gmx sorient
===========

Synopsis
--------

.. parsed-literal::

    gmx sorient [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-no` :emphasis:`[<.xvg>]`] [:strong:`-ro` :emphasis:`[<.xvg>]`]
                [:strong:`-co` :emphasis:`[<.xvg>]`] [:strong:`-rc` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
                [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-[no]com`] [:strong:`-[no]v23`]
                [:strong:`-rmin` :emphasis:`<real>`] [:strong:`-rmax` :emphasis:`<real>`] [:strong:`-cbin` :emphasis:`<real>`]
                [:strong:`-rbin` :emphasis:`<real>`] [:strong:`-[no]pbc`]

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

``gmx sorient`` analyzes solvent orientation around solutes.
It calculates two angles between the vector from one or more
reference positions to the first atom of each solvent molecule:

 * theta_1: the angle with the vector from the first atom of the solvent
   molecule to the midpoint between atoms 2 and 3.
 * theta_2: the angle with the normal of the solvent plane, defined by the
   same three atoms, or, when the option ``-v23`` is set,
   the angle with the vector between atoms 2 and 3.

The reference can be a set of atoms or
the center of mass of a set of atoms. The group of solvent atoms should
consist of 3 atoms per solvent molecule.
Only solvent molecules between ``-rmin`` and ``-rmax`` are
considered for ``-o`` and ``-no`` each frame.

``-o``: distribution of cos(theta_1) for rmin<=r<=rmax.

``-no``: distribution of cos(theta_2) for rmin<=r<=rmax.

``-ro``: <cos(theta_1)> and <3cos(^2theta_2)-1> as a function of the
distance.

``-co``: the sum over all solvent molecules within distance r
of cos(theta_1) and 3cos(^2(theta_2)-1) as a function of r.

``-rc``: the distribution of the solvent molecules as a function of r

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

Options to specify output files:

``-o`` [<.xvg>] (sori.xvg)
    xvgr/xmgr file
``-no`` [<.xvg>] (snor.xvg)
    xvgr/xmgr file
``-ro`` [<.xvg>] (sord.xvg)
    xvgr/xmgr file
``-co`` [<.xvg>] (scum.xvg)
    xvgr/xmgr file
``-rc`` [<.xvg>] (scount.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)
``-[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]com``  (no)
    Use the center of mass as the reference position
``-[no]v23``  (no)
    Use the vector between atoms 2 and 3
``-rmin`` <real> (0)
    Minimum distance (nm)
``-rmax`` <real> (0.5)
    Maximum distance (nm)
``-cbin`` <real> (0.02)
    Binwidth for the cosine
``-rbin`` <real> (0.02)
    Binwidth for r (nm)
``-[no]pbc``  (no)
    Check PBC for the center of mass calculation. Only necessary when your reference group consists of several molecules.

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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