.. _gmx bundle:

gmx bundle
==========

Synopsis
--------

.. parsed-literal::

    gmx bundle [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
               [:strong:`-ol` :emphasis:`[<.xvg>]`] [:strong:`-od` :emphasis:`[<.xvg>]`] [:strong:`-oz` :emphasis:`[<.xvg>]`]
               [:strong:`-ot` :emphasis:`[<.xvg>]`] [:strong:`-otr` :emphasis:`[<.xvg>]`] [:strong:`-otl` :emphasis:`[<.xvg>]`]
               [:strong:`-ok` :emphasis:`[<.xvg>]`] [:strong:`-okr` :emphasis:`[<.xvg>]`] [:strong:`-okl` :emphasis:`[<.xvg>]`]
               [:strong:`-oa` :emphasis:`[<.pdb>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
               [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-na` :emphasis:`<int>`] [:strong:`-[no]z`]

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

``gmx bundle`` analyzes bundles of axes. The axes can be for instance
helix axes. The program reads two index groups and divides both
of them in ``-na`` parts. The centers of mass of these parts
define the tops and bottoms of the axes.
Several quantities are written to file:
the axis length, the distance and the z-shift of the axis mid-points
with respect to the average center of all axes, the total tilt,
the radial tilt and the lateral tilt with respect to the average axis.

With options ``-ok``, ``-okr`` and ``-okl`` the total,
radial and lateral kinks of the axes are plotted. An extra index
group of kink atoms is required, which is also divided into ``-na``
parts. The kink angle is defined as the angle between the kink-top and
the bottom-kink vectors.

With option ``-oa`` the top, mid (or kink when ``-ok`` is set)
and bottom points of each axis
are written to a :ref:`.pdb <pdb>` file each frame. The residue numbers correspond
to the axis numbers. When viewing this file with Rasmol, use the
command line option ``-nmrpdb``, and type ``set axis true`` to
display the reference axis.

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:

``-ol`` [<.xvg>] (bun_len.xvg)
    xvgr/xmgr file
``-od`` [<.xvg>] (bun_dist.xvg)
    xvgr/xmgr file
``-oz`` [<.xvg>] (bun_z.xvg)
    xvgr/xmgr file
``-ot`` [<.xvg>] (bun_tilt.xvg)
    xvgr/xmgr file
``-otr`` [<.xvg>] (bun_tiltr.xvg)
    xvgr/xmgr file
``-otl`` [<.xvg>] (bun_tiltl.xvg)
    xvgr/xmgr file
``-ok`` [<.xvg>] (bun_kink.xvg) (Optional)
    xvgr/xmgr file
``-okr`` [<.xvg>] (bun_kinkr.xvg) (Optional)
    xvgr/xmgr file
``-okl`` [<.xvg>] (bun_kinkl.xvg) (Optional)
    xvgr/xmgr file
``-oa`` [<.pdb>] (axes.pdb) (Optional)
    Protein data bank 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
``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-na`` <int> (0)
    Number of axes
``-[no]z``  (no)
    Use the *z*-axis as reference instead of the average axis

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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