.. _gmx morph:

gmx morph
=========

Synopsis
--------

.. parsed-literal::

    gmx morph [:strong:`-f1` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-f2` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`]
              [:strong:`-o` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-or` :emphasis:`[<.xvg>]`] [:strong:`-[no]w`]
              [:strong:`-xvg` :emphasis:`<enum>`] [:strong:`-ninterm` :emphasis:`<int>`] [:strong:`-first` :emphasis:`<real>`]
              [:strong:`-last` :emphasis:`<real>`] [:strong:`-[no]fit`]

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

``gmx morph`` does a linear interpolation of conformations in order to
create intermediates. Of course these are completely unphysical, but
that you may try to justify yourself. Output is in the form of a
generic trajectory. The number of intermediates can be controlled with
the ``-ninterm`` flag. The first and last flag correspond to the way of
interpolating: 0 corresponds to input structure 1 while
1 corresponds to input structure 2.
If you specify ``-first`` < 0 or ``-last`` > 1 extrapolation will be
on the path from input structure x_1 to x_2. In general, the coordinates
of the intermediate x(i) out of N total intermediates correspond to:

x(i) = x_1 + (first+(i/(N-1))*(last-first))*(x_2-x_1)

Finally the RMSD with respect to both input structures can be computed
if explicitly selected (``-or`` option). In that case, an index file may be
read to select the group from which the RMS is computed.

Options
-------

Options to specify input files:

``-f1`` [<.gro/.g96/...>] (conf1.gro)
    Structure file: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`tpr`
``-f2`` [<.gro/.g96/...>] (conf2.gro)
    Structure file: :ref:`gro` :ref:`g96` :ref:`pdb` brk ent esp :ref:`tpr`
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file

Options to specify output files:

``-o`` [<.xtc/.trr/...>] (interm.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`cpt` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`
``-or`` [<.xvg>] (rms-interm.xvg) (Optional)
    xvgr/xmgr file

Other options:

``-[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
``-ninterm`` <int> (11)
    Number of intermediates
``-first`` <real> (0)
    Corresponds to first generated structure (0 is input x_1, see above)
``-last`` <real> (1)
    Corresponds to last generated structure (1 is input x_2, see above)
``-[no]fit``  (yes)
    Do a least squares fit of the second to the first structure before interpolating

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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