.. _gmx trajectory:

gmx trajectory
==============

Synopsis
--------

.. parsed-literal::

    gmx trajectory [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`]
                 [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-ox` :emphasis:`[<.xvg>]`] [:strong:`-ov` :emphasis:`[<.xvg>]`]
                 [:strong:`-of` :emphasis:`[<.xvg>]`] [:strong:`-b` :emphasis:`<time>`] [:strong:`-e` :emphasis:`<time>`] [:strong:`-dt` :emphasis:`<time>`]
                 [:strong:`-tu` :emphasis:`<enum>`] [:strong:`-fgroup` :emphasis:`<selection>`] [:strong:`-xvg` :emphasis:`<enum>`]
                 [:strong:`-[no]rmpbc`] [:strong:`-[no]pbc`] [:strong:`-sf` :emphasis:`<file>`] [:strong:`-selrpos` :emphasis:`<enum>`]
                 [:strong:`-seltype` :emphasis:`<enum>`] [:strong:`-select` :emphasis:`<selection>`] [:strong:`-[no]x`]
                 [:strong:`-[no]y`] [:strong:`-[no]z`] [:strong:`-[no]len`]

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

``gmx trajectory`` plots coordinates, velocities, and/or forces for
provided selections. By default, the X, Y, and Z components for
the requested vectors are plotted, but specifying one or more of
``-len``, ``-x``, ``-y``, and ``-z`` overrides this.

For dynamic selections, currently the values are written out for
all positions that the selection could select.

Options
-------

Options to specify input files:

``-f`` [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Input trajectory or single configuration: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-s`` [<.tpr/.gro/...>] (topol.tpr) (Optional)
    Input structure: :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Extra index groups

Options to specify output files:

``-ox`` [<.xvg>] (coord.xvg) (Optional)
    Coordinates for each position as a function of time
``-ov`` [<.xvg>] (veloc.xvg) (Optional)
    Velocities for each position as a function of time
``-of`` [<.xvg>] (force.xvg) (Optional)
    Forces for each position as a function of time

Other options:

``-b`` <time> (0)
    First frame (ps) to read from trajectory
``-e`` <time> (0)
    Last frame (ps) to read from trajectory
``-dt`` <time> (0)
    Only use frame if t MOD dt == first time (ps)
``-tu`` <enum> (ps)
    Unit for time values: fs, ps, ns, us, ms, s
``-fgroup`` <selection>
    Atoms stored in the trajectory file (if not set, assume first N atoms)
``-xvg`` <enum> (xmgrace)
    Plot formatting: none, xmgrace, xmgr
``-[no]rmpbc``  (yes)
    Make molecules whole for each frame
``-[no]pbc``  (yes)
    Use periodic boundary conditions for distance calculation
``-sf`` <file>
    Provide selections from files
``-selrpos`` <enum> (atom)
    Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-seltype`` <enum> (atom)
    Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
``-select`` <selection>
    Selections to analyze
``-[no]x``  (yes)
    Plot X component
``-[no]y``  (yes)
    Plot Y component
``-[no]z``  (yes)
    Plot Z component
``-[no]len``  (no)
    Plot vector length

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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