.. _gmx principal:

gmx principal
=============

Synopsis
--------

.. parsed-literal::

    gmx principal [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`]
                 [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-a1` :emphasis:`[<.xvg>]`] [:strong:`-a2` :emphasis:`[<.xvg>]`]
                 [:strong:`-a3` :emphasis:`[<.xvg>]`] [:strong:`-om` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`]
                 [:strong:`-dt` :emphasis:`<time>`] [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-[no]w`] [:strong:`-xvg` :emphasis:`<enum>`]
                 [:strong:`-[no]foo`]

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

``gmx principal`` calculates the three principal axes of inertia for a group
of atoms. NOTE: Old versions of GROMACS wrote the output data in a
strange transposed way. As of GROMACS 5.0, the output file paxis1.dat
contains the x/y/z components of the first (major) principal axis for
each frame, and similarly for the middle and minor axes in paxis2.dat
and paxis3.dat.

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:

``-a1`` [<.xvg>] (paxis1.xvg)
    xvgr/xmgr file
``-a2`` [<.xvg>] (paxis2.xvg)
    xvgr/xmgr file
``-a3`` [<.xvg>] (paxis3.xvg)
    xvgr/xmgr file
``-om`` [<.xvg>] (moi.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)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-[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]foo``  (no)
    Dummy option to avoid empty array

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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