.. _gmx nmens:

gmx nmens
=========

Synopsis
--------

.. parsed-literal::

    gmx nmens [:strong:`-v` :emphasis:`[<.trr/.cpt/...>]`] [:strong:`-e` :emphasis:`[<.xvg>]`] [:strong:`-s` :emphasis:`[<.tpr/.gro/...>]`]
              [:strong:`-n` :emphasis:`[<.ndx>]`] [:strong:`-o` :emphasis:`[<.xtc/.trr/...>]`] [:strong:`-xvg` :emphasis:`<enum>`]
              [:strong:`-temp` :emphasis:`<real>`] [:strong:`-seed` :emphasis:`<int>`] [:strong:`-num` :emphasis:`<int>`] [:strong:`-first` :emphasis:`<int>`]
              [:strong:`-last` :emphasis:`<int>`]

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

``gmx nmens`` generates an ensemble around an average structure
in a subspace that is defined by a set of normal modes (eigenvectors).
The eigenvectors are assumed to be mass-weighted.
The position along each eigenvector is randomly taken from a Gaussian
distribution with variance kT/eigenvalue.

By default the starting eigenvector is set to 7, since the first six
normal modes are the translational and rotational degrees of freedom.

Options
-------

Options to specify input files:

``-v`` [<.trr/.cpt/...>] (eigenvec.trr)
    Full precision trajectory: :ref:`trr` :ref:`cpt` :ref:`tng`
``-e`` [<.xvg>] (eigenval.xvg)
    xvgr/xmgr file
``-s`` [<.tpr/.gro/...>] (topol.tpr)
    Structure+mass(db): :ref:`tpr` :ref:`gro` :ref:`g96` :ref:`pdb` brk ent
``-n`` [<.ndx>] (index.ndx) (Optional)
    Index file

Options to specify output files:

``-o`` [<.xtc/.trr/...>] (ensemble.xtc)
    Trajectory: :ref:`xtc` :ref:`trr` :ref:`gro` :ref:`g96` :ref:`pdb` :ref:`tng`

Other options:

``-xvg`` <enum> (xmgrace)
    xvg plot formatting: xmgrace, xmgr, none
``-temp`` <real> (300)
    Temperature in Kelvin
``-seed`` <int> (0)
    Random seed (0 means generate)
``-num`` <int> (100)
    Number of structures to generate
``-first`` <int> (7)
    First eigenvector to use (-1 is select)
``-last`` <int> (-1)
    Last eigenvector to use (-1 is till the last)

.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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