.. _gmx traj:

gmx traj
========

Synopsis
--------

.. parsed-literal::

    gmx traj [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
             [:strong:`-ox` :emphasis:`[<.xvg>]`] [:strong:`-oxt` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-ov` :emphasis:`[<.xvg>]`]
             [:strong:`-of` :emphasis:`[<.xvg>]`] [:strong:`-ob` :emphasis:`[<.xvg>]`] [:strong:`-ot` :emphasis:`[<.xvg>]`] [:strong:`-ekt` :emphasis:`[<.xvg>]`]
             [:strong:`-ekr` :emphasis:`[<.xvg>]`] [:strong:`-vd` :emphasis:`[<.xvg>]`] [:strong:`-cv` :emphasis:`[<.pdb>]`] [:strong:`-cf` :emphasis:`[<.pdb>]`]
             [:strong:`-av` :emphasis:`[<.xvg>]`] [:strong:`-af` :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]com`]
             [:strong:`-[no]pbc`] [:strong:`-[no]mol`] [:strong:`-[no]nojump`] [:strong:`-[no]x`] [:strong:`-[no]y`]
             [:strong:`-[no]z`] [:strong:`-ng` :emphasis:`<int>`] [:strong:`-[no]len`] [:strong:`-[no]fp`] [:strong:`-bin` :emphasis:`<real>`]
             [:strong:`-ctime` :emphasis:`<real>`] [:strong:`-scale` :emphasis:`<real>`]

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

``gmx traj`` plots coordinates, velocities, forces and/or the box.
With ``-com`` the coordinates, velocities and forces are
calculated for the center of mass of each group.
When ``-mol`` is set, the numbers in the index file are
interpreted as molecule numbers and the same procedure as with
``-com`` is used for each molecule.

Option ``-ot`` plots the temperature of each group,
provided velocities are present in the trajectory file.
No corrections are made for constrained degrees of freedom!
This implies ``-com``.

Options ``-ekt`` and ``-ekr`` plot the translational and
rotational kinetic energy of each group,
provided velocities are present in the trajectory file.
This implies ``-com``.

Options ``-cv`` and ``-cf`` write the average velocities
and average forces as temperature factors to a :ref:`.pdb <pdb>` file with
the average coordinates or the coordinates at ``-ctime``.
The temperature factors are scaled such that the maximum is 10.
The scaling can be changed with the option ``-scale``.
To get the velocities or forces of one
frame set both ``-b`` and ``-e`` to the time of
desired frame. When averaging over frames you might need to use
the ``-nojump`` option to obtain the correct average coordinates.
If you select either of these option the average force and velocity
for each atom are written to an :ref:`.xvg <xvg>` file as well
(specified with ``-av`` or ``-af``).

Option ``-vd`` computes a velocity distribution, i.e. the
norm of the vector is plotted. In addition in the same graph
the kinetic energy distribution is given.

See :doc:`gmx trajectory <gmx-trajectory>` for plotting similar data for selections.

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:

``-ox`` [<.xvg>] (coord.xvg) (Optional)
    xvgr/xmgr file
``-oxt`` [<.xtc/.trr/...>] (coord.xtc) (Optional)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-ov`` [<.xvg>] (veloc.xvg) (Optional)
    xvgr/xmgr file
``-of`` [<.xvg>] (force.xvg) (Optional)
    xvgr/xmgr file
``-ob`` [<.xvg>] (box.xvg) (Optional)
    xvgr/xmgr file
``-ot`` [<.xvg>] (temp.xvg) (Optional)
    xvgr/xmgr file
``-ekt`` [<.xvg>] (ektrans.xvg) (Optional)
    xvgr/xmgr file
``-ekr`` [<.xvg>] (ekrot.xvg) (Optional)
    xvgr/xmgr file
``-vd`` [<.xvg>] (veldist.xvg) (Optional)
    xvgr/xmgr file
``-cv`` [<.pdb>] (veloc.pdb) (Optional)
    Protein data bank file
``-cf`` [<.pdb>] (force.pdb) (Optional)
    Protein data bank file
``-av`` [<.xvg>] (all_veloc.xvg) (Optional)
    xvgr/xmgr file
``-af`` [<.xvg>] (all_force.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)
``-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]com``  (no)
    Plot data for the com of each group
``-[no]pbc``  (yes)
    Make molecules whole for COM
``-[no]mol``  (no)
    Index contains molecule numbers instead of atom numbers
``-[no]nojump``  (no)
    Remove jumps of atoms across the box
``-[no]x``  (yes)
    Plot X-component
``-[no]y``  (yes)
    Plot Y-component
``-[no]z``  (yes)
    Plot Z-component
``-ng`` <int> (1)
    Number of groups to consider
``-[no]len``  (no)
    Plot vector length
``-[no]fp``  (no)
    Full precision output
``-bin`` <real> (1)
    Binwidth for velocity histogram (nm/ps)
``-ctime`` <real> (-1)
    Use frame at this time for x in ``-cv`` and ``-cf`` instead of the average x
``-scale`` <real> (0)
    Scale factor for :ref:`.pdb <pdb>` output, 0 is autoscale

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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