.. _gmx order:

gmx order
=========

Synopsis
--------

.. parsed-literal::

    gmx order [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-nr` :emphasis:`[<.ndx>]`]
              [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-o` :emphasis:`[<.xvg>]`] [:strong:`-od` :emphasis:`[<.xvg>]`] [:strong:`-ob` :emphasis:`[<.pdb>]`]
              [:strong:`-os` :emphasis:`[<.xvg>]`] [:strong:`-Sg` :emphasis:`[<.xvg>]`] [:strong:`-Sk` :emphasis:`[<.xvg>]`]
              [:strong:`-Sgsl` :emphasis:`[<.xvg>]`] [:strong:`-Sksl` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
              [:strong:`-dt` :emphasis:`<time>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-d` :emphasis:`<enum>`] [:strong:`-sl` :emphasis:`<int>`]
              [:strong:`-[no]szonly`] [:strong:`-[no]unsat`] [:strong:`-[no]permolecule`] [:strong:`-[no]radial`]
              [:strong:`-[no]calcdist`]

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

``gmx order`` computes the order parameter per atom for carbon tails. For atom i the
vector i-1, i+1 is used together with an axis.
The index file should contain only the groups to be used for calculations,
with each group of equivalent carbons along the relevant acyl chain in its own
group. There should not be any generic groups (like System, Protein) in the index
file to avoid confusing the program (this is not relevant to tetrahedral order
parameters however, which only work for water anyway).

``gmx order`` can also give all
diagonal elements of the order tensor and even calculate the deuterium
order parameter Scd (default). If the option ``-szonly`` is given, only one
order tensor component (specified by the ``-d`` option) is given and the
order parameter per slice is calculated as well. If ``-szonly`` is not
selected, all diagonal elements and the deuterium order parameter is
given.

The tetrahedrality order parameters can be determined
around an 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.

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

Options to specify output files:

``-o`` [<.xvg>] (order.xvg)
    xvgr/xmgr file
``-od`` [<.xvg>] (deuter.xvg)
    xvgr/xmgr file
``-ob`` [<.pdb>] (eiwit.pdb) (Optional)
    Protein data bank file
``-os`` [<.xvg>] (sliced.xvg)
    xvgr/xmgr file
``-Sg`` [<.xvg>] (sg-ang.xvg) (Optional)
    xvgr/xmgr file
``-Sk`` [<.xvg>] (sk-dist.xvg) (Optional)
    xvgr/xmgr file
``-Sgsl`` [<.xvg>] (sg-ang-slice.xvg) (Optional)
    xvgr/xmgr file
``-Sksl`` [<.xvg>] (sk-dist-slice.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)
``-[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
``-d`` <enum> (z)
    Direction of the normal on the membrane: z, x, y
``-sl`` <int> (1)
    Calculate order parameter as function of box length, dividing the box into this number of slices.
``-[no]szonly``  (no)
    Only give Sz element of order tensor. (axis can be specified with ``-d``)
``-[no]unsat``  (no)
    Calculate order parameters for unsaturated carbons. Note that this cannot be mixed with normal order parameters.
``-[no]permolecule``  (no)
    Compute per-molecule Scd order parameters
``-[no]radial``  (no)
    Compute a radial membrane normal
``-[no]calcdist``  (no)
    Compute distance from a reference

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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