.. _gmx convert-tpr:

gmx convert-tpr
===============
Synopsis
--------
.. parsed-literal::

    gmx convert-tpr [:strong:`-s` :emphasis:`[<.tpr>]`] [:strong:`-f` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-e` :emphasis:`[<.edr>]`]
                 [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.tpr>]`] [:strong:`-extend` :emphasis:`<real>`]
                 [:strong:`-until` :emphasis:`<real>`] [:strong:`-nsteps` :emphasis:`<int>`] [:strong:`-time` :emphasis:`<real>`]
                 [:strong:`-[no]zeroq`] [:strong:`-[no]vel`] [:strong:`-[no]cont`]
                 [:strong:`-init_fep_state` :emphasis:`<int>`]

Description
-----------
``gmx convert-tpr`` can edit run input files in four ways.

**1.** by modifying the number of steps in a run input file
with options ``-extend``, ``-until`` or ``-nsteps``
(nsteps=-1 means unlimited number of steps)

**2.** (OBSOLETE) by creating a run input file
for a continuation run when your simulation has crashed due to e.g.
a full disk, or by making a continuation run input file.
This option is obsolete, since mdrun now writes and reads
checkpoint files.
**Note** that a frame with coordinates and velocities is needed.
When pressure and/or Nose-Hoover temperature coupling is used
an energy file can be supplied to get an exact continuation
of the original run.

**3.** by creating a .tpx file for a subset of your original
tpx file, which is useful when you want to remove the solvent from
your .tpx file, or when you want to make e.g. a pure Calpha .tpx file.
Note that you may need to use ``-nsteps -1`` (or similar) to get
this to work.
**WARNING: this .tpx file is not fully functional**.

**4.** by setting the charges of a specified group
to zero. This is useful when doing free energy estimates
using the LIE (Linear Interaction Energy) method.

Options
-------
Options to specify input files:

``-s`` [<.tpr>] (topol.tpr)
    Portable xdr run input file
``-f`` [<.trr/.cpt/...>] (traj.trr) (Optional)
    Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng`
``-e`` [<.edr>] (ener.edr) (Optional)
    Energy file
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file

Options to specify output files:

``-o`` [<.tpr>] (tprout.tpr)
    Portable xdr run input file

Other options:

``-extend`` <real> (0)
    Extend runtime by this amount (ps)
``-until`` <real> (0)
    Extend runtime until this ending time (ps)
``-nsteps`` <int> (0)
    Change the number of steps
``-time`` <real> (-1)
    Continue from frame at this time (ps) instead of the last frame
``-[no]zeroq``  (no)
    Set the charges of a group (from the index) to zero
``-[no]vel``  (yes)
    Require velocities from trajectory
``-[no]cont``  (yes)
    For exact continuation, the constraints should not be applied before the first step
``-init_fep_state`` <int> (0)
    fep state to initialize from


.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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