.. _gmx hydorder:

gmx hydorder
============

Synopsis
--------

.. parsed-literal::

    gmx hydorder [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-s` :emphasis:`[<.tpr>]`]
                 [:strong:`-o` :emphasis:`[<.xpm> [...]]`] [:strong:`-or` :emphasis:`[<.out> [...]]`]
                 [:strong:`-Spect` :emphasis:`[<.out> [...]]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
                 [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-d` :emphasis:`<enum>`] [:strong:`-bw` :emphasis:`<real>`]
                 [:strong:`-sgang1` :emphasis:`<real>`] [:strong:`-sgang2` :emphasis:`<real>`] [:strong:`-tblock` :emphasis:`<int>`]
                 [:strong:`-nlevel` :emphasis:`<int>`]

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

``gmx hydorder`` computes the tetrahedrality order parameters around a
given atom. Both angle an distance order parameters are calculated. See
P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518.
for more details.

``gmx hydorder`` calculates the order parameter in a 3d-mesh in the box, and
with 2 phases in the box gives the user the option to define a 2D interface in time
separating the faces by specifying parameters ``-sgang1`` and
``-sgang2`` (it is important to select these judiciously).

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`
``-n`` [<.ndx>] (index.ndx)
    Index file
``-s`` [<.tpr>] (topol.tpr)
    Portable xdr run input file

Options to specify output files:

``-o`` [<.xpm> [...]] (intf.xpm)
    X PixMap compatible matrix file
``-or`` [<.out> [...]] (raw.out) (Optional)
    Generic output file
``-Spect`` [<.out> [...]] (intfspect.out) (Optional)
    Generic output 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
``-d`` <enum> (z)
    Direction of the normal on the membrane: z, x, y
``-bw`` <real> (1)
    Binwidth of box mesh
``-sgang1`` <real> (1)
    tetrahedral angle parameter in Phase 1 (bulk)
``-sgang2`` <real> (1)
    tetrahedral angle parameter in Phase 2 (bulk)
``-tblock`` <int> (1)
    Number of frames in one time-block average
``-nlevel`` <int> (100)
    Number of Height levels in 2D - XPixMaps

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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