.. _gmx trjorder:

gmx trjorder
============

Synopsis
--------

.. parsed-literal::

    gmx trjorder [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
                 [:strong:`-o` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-nshell` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`]
                 [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-na` :emphasis:`<int>`]
                 [:strong:`-da` :emphasis:`<int>`] [:strong:`-[no]com`] [:strong:`-r` :emphasis:`<real>`] [:strong:`-[no]z`]

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

``gmx trjorder`` orders molecules according to the smallest distance
to atoms in a reference group
or on z-coordinate (with option ``-z``).
With distance ordering, it will ask for a group of reference
atoms and a group of molecules. For each frame of the trajectory
the selected molecules will be reordered according to the shortest
distance between atom number ``-da`` in the molecule and all the
atoms in the reference group. The center of mass of the molecules can
be used instead of a reference atom by setting ``-da`` to 0.
All atoms in the trajectory are written
to the output trajectory.

``gmx trjorder`` can be useful for e.g. analyzing the n waters closest to a
protein.
In that case the reference group would be the protein and the group
of molecules would consist of all the water atoms. When an index group
of the first n waters is made, the ordered trajectory can be used
with any GROMACS program to analyze the n closest waters.

If the output file is a :ref:`.pdb <pdb>` file, the distance to the reference target
will be stored in the B-factor field in order to color with e.g. Rasmol.

With option ``-nshell`` the number of molecules within a shell
of radius ``-r`` around the reference group are printed.

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`` [<.xtc/.trr/...>] (ordered.xtc) (Optional)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-nshell`` [<.xvg>] (nshell.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)
``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-na`` <int> (3)
    Number of atoms in a molecule
``-da`` <int> (1)
    Atom used for the distance calculation, 0 is COM
``-[no]com``  (no)
    Use the distance to the center of mass of the reference group
``-r`` <real> (0)
    Cutoff used for the distance calculation when computing the number of molecules in a shell around e.g. a protein
``-[no]z``  (no)
    Order molecules on z-coordinate

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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