.. _gmx genrestr:

gmx genrestr
============

Synopsis
--------

.. parsed-literal::

    gmx genrestr [:strong:`-f` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.itp>]`]
                 [:strong:`-of` :emphasis:`[<.ndx>]`] [:strong:`-fc` :emphasis:`<vector>`] [:strong:`-freeze` :emphasis:`<real>`]
                 [:strong:`-[no]disre`] [:strong:`-disre_dist` :emphasis:`<real>`] [:strong:`-disre_frac` :emphasis:`<real>`]
                 [:strong:`-disre_up2` :emphasis:`<real>`] [:strong:`-cutoff` :emphasis:`<real>`] [:strong:`-[no]constr`]

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

``gmx genrestr`` produces an #include file for a topology containing
a list of atom numbers and three force constants for the
*x*-, *y*-, and *z*-direction based on
the contents of the ``-f`` file. A single isotropic force constant may
be given on the command line instead of three components.

WARNING: Position restraints are interactions within molecules, therefore
they must be included within the correct ``[ moleculetype ]``
block in the topology. The atom indices within the
``[ position_restraints ]`` block must be within the range of the
atom indices for that molecule type. Since the atom numbers in every
moleculetype in the topology start at 1 and the numbers in the input file
for ``gmx genrestr`` number consecutively from 1, ``gmx genrestr`` will only
produce a useful file for the first molecule. You may wish to
edit the resulting index file to remove the lines for later atoms,
or construct a suitable index group to provide
as input to ``gmx genrestr``.

The ``-of`` option produces an index file that can be used for
freezing atoms. In this case, the input file must be a :ref:`.pdb <pdb>` file.

With the ``-disre`` option, half a matrix of distance restraints
is generated instead of position restraints. With this matrix, that
one typically would apply to Calpha atoms in a protein, one can
maintain the overall conformation of a protein without tieing it to
a specific position (as with position restraints).

Options
-------

Options to specify input files:

``-f`` [<.gro/.g96/...>] (conf.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`` [<.itp>] (posre.itp)
    Include file for topology
``-of`` [<.ndx>] (freeze.ndx) (Optional)
    Index file

Other options:

``-fc`` <vector> (1000 1000 1000)
    Force constants (kJ/mol nm^2)
``-freeze`` <real> (0)
    If the ``-of`` option or this one is given an index file will be written containing atom numbers of all atoms that have a B-factor less than the level given here
``-[no]disre``  (no)
    Generate a distance restraint matrix for all the atoms in index
``-disre_dist`` <real> (0.1)
    Distance range around the actual distance for generating distance restraints
``-disre_frac`` <real> (0)
    Fraction of distance to be used as interval rather than a fixed distance. If the fraction of the distance that you specify here is less than the distance given in the previous option, that one is used instead.
``-disre_up2`` <real> (1)
    Distance between upper bound for distance restraints, and the distance at which the force becomes constant (see manual)
``-cutoff`` <real> (-1)
    Only generate distance restraints for atoms pairs within cutoff (nm)
``-[no]constr``  (no)
    Generate a constraint matrix rather than distance restraints. Constraints of type 2 will be generated that do generate exclusions.

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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