.. _gmx dump:

gmx dump
========

Synopsis
--------

.. parsed-literal::

    gmx dump [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-f` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-e` :emphasis:`[<.edr>]`]
             [:strong:`-cp` :emphasis:`[<.cpt>]`] [:strong:`-p` :emphasis:`[<.top>]`] [:strong:`-mtx` :emphasis:`[<.mtx>]`] [:strong:`-om` :emphasis:`[<.mdp>]`]
             [:strong:`-[no]nr`] [:strong:`-[no]sys`]

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

``gmx dump`` reads a run input file (:ref:`.tpr <tpr>`),
a trajectory (:ref:`.trr <trr>`/:ref:`.xtc <xtc>`/``/tng``), an energy
file (:ref:`.edr <edr>`) or a checkpoint file (:ref:`.cpt <cpt>`)
and prints that to standard output in a readable format.
This program is essential for checking your run input file in case of
problems.

The program can also preprocess a topology to help finding problems.
Note that currently setting ``GMXLIB`` is the only way to customize
directories used for searching include files.

Options
-------

Options to specify input files:

``-s`` [<.tpr>] (topol.tpr) (Optional)
    Portable xdr run input file
``-f`` [<.xtc/.trr/...>] (traj.xtc) (Optional)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-e`` [<.edr>] (ener.edr) (Optional)
    Energy file
``-cp`` [<.cpt>] (state.cpt) (Optional)
    Checkpoint file
``-p`` [<.top>] (topol.top) (Optional)
    Topology file
``-mtx`` [<.mtx>] (hessian.mtx) (Optional)
    Hessian matrix

Options to specify output files:

``-om`` [<.mdp>] (grompp.mdp) (Optional)
    grompp input file with MD parameters

Other options:

``-[no]nr``  (yes)
    Show index numbers in output (leaving them out makes comparison easier, but creates a useless topology)
``-[no]sys``  (no)
    List the atoms and bonded interactions for the whole system instead of for each molecule type

Known Issues
------------

* Position restraint output from -sys -s is broken

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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