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update group2ndx/ndx2group docs

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Axel Kohlmeyer
2024-06-17 15:02:43 -04:00
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doc/src/group2ndx.rst
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@ -34,21 +34,54 @@ Description
Write or read a Gromacs style index file in text format that associates Write or read a Gromacs style index file in text format that associates
atom IDs with the corresponding group definitions. This index file can be atom IDs with the corresponding group definitions. This index file can be
used with in combination with Gromacs analysis tools or to import group used with in combination with Gromacs analysis tools or to import group
definitions into the :doc:`fix colvars <fix_colvars>` input file. It can definitions into the :doc:`fix colvars <fix_colvars>` input file.
also be used to save and restore group definitions for static groups.
It can also be used to save and restore group definitions for static groups
using the individual atom IDs. This may be important if the original
group definition depends on a region or otherwise on the geometry and thus
cannot be easily recreated.
Another application would be to import atom groups defined for Gromacs
simulation into LAMMPS. When translating Gromacs topology and geometry
data to LAMMPS.
The *group2ndx* command will write group definitions to an index file. The *group2ndx* command will write group definitions to an index file.
Without specifying any group IDs, all groups will be written to the index Without specifying any group IDs, all groups will be written to the
file. When specifying group IDs, only those groups will be written to the index file. When specifying group IDs, only those groups will be
index file. In order to follow the Gromacs conventions, the group *all* written to the index file. In order to follow the Gromacs conventions,
will be renamed to *System* in the index file. the group *all* will be renamed to *System* in the index file.
The *ndx2group* command will create of update group definitions from those The *ndx2group* command will create of update group definitions from
stored in an index file. Without specifying any group IDs, all groups except those stored in an index file. Without specifying any group IDs, all
*System* will be read from the index file and the corresponding groups groups except *System* will be read from the index file and the
recreated. If a group of the same name already exists, it will be completely corresponding groups recreated. If a group of the same name already
reset. When specifying group IDs, those groups, if present, will be read exists, it will be completely reset. When specifying group IDs, those
from the index file and restored. groups, if present, will be read from the index file and restored.
File Format
"""""""""""
The file format is equivalent and compatible with what is produced by
the `Gromacs make_ndx command <https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_.
and follows the `Gromacs definition of an ndx file <https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx>`_
Each group definition begins with the group name in square brackets with
blanks, e.g. \[ water \] and is then followed by the list of atom
indices, which may be spread over multiple lines. Here is a small
example file:
.. code-block:: ini
[ Oxygen ]
1 4 7
[ Hydrogen ]
2 3 5 6
8 9
[ Water ]
1 2 3 4 5 6 7 8 9
The index file defines 3 groups: Oxygen, Hydrogen, and Water and the
latter happens to be the union of the first two.
---------- ----------