.. _gmx make_ndx:

gmx make_ndx
============
Synopsis
--------
.. parsed-literal::

    gmx make_ndx [:strong:`-f` :emphasis:`[<.gro/.g96/...>]`] [:strong:`-n` :emphasis:`[<.ndx> [...]]`] [:strong:`-o` :emphasis:`[<.ndx>]`]
                 [:strong:`-natoms` :emphasis:`<int>`] [:strong:`-[no]twin`]

Description
-----------
Index groups are necessary for almost every GROMACS program.
All these programs can generate default index groups. You ONLY
have to use ``gmx make_ndx`` when you need SPECIAL index groups.
There is a default index group for the whole system, 9 default
index groups for proteins, and a default index group
is generated for every other residue name.

When no index file is supplied, also ``gmx make_ndx`` will generate the
default groups.
With the index editor you can select on atom, residue and chain names
and numbers.
When a run input file is supplied you can also select on atom type.
You can use NOT, AND and OR, you can split groups
into chains, residues or atoms. You can delete and rename groups.

The atom numbering in the editor and the index file starts at 1.

The ``-twin`` switch duplicates all index groups with an offset of
``-natoms``, which is useful for Computational Electrophysiology
double-layer membrane setups.

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

``-f`` [<.gro/.g96/...>] (conf.gro) (Optional)
    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`` [<.ndx>] (index.ndx)
    Index file

Other options:

``-natoms`` <int> (0)
    set number of atoms (default: read from coordinate or index file)
``-[no]twin``  (no)
    Duplicate all index groups with an offset of -natoms


.. only:: man

   See also
   --------

   :manpage:`gmx(1)`

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