107 lines
3.1 KiB
ReStructuredText
107 lines
3.1 KiB
ReStructuredText
.. index:: group2ndx
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.. index:: ndx2group
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group2ndx command
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=================
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ndx2group command
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=================
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Syntax
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""""""
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.. code-block:: LAMMPS
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group2ndx file args
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ndx2group file args
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* file = name of index file to write out or read in
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* args = zero or more group IDs may be appended
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Examples
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""""""""
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.. code-block:: LAMMPS
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group2ndx allindex.ndx
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group2ndx someindex.ndx upper lower mobile
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ndx2group someindex.ndx
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ndx2group someindex.ndx mobile
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Description
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"""""""""""
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Write or read a Gromacs style index file in text format that associates
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atom IDs with the corresponding group definitions. This index file can be
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used with in combination with Gromacs analysis tools or to import group
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definitions into the :doc:`fix colvars <fix_colvars>` input file.
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It can also be used to save and restore group definitions for static groups
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using the individual atom IDs. This may be important if the original
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group definition depends on a region or otherwise on the geometry and thus
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cannot be easily recreated.
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Another application would be to import atom groups defined for Gromacs
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simulation into LAMMPS. When translating Gromacs topology and geometry
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data to LAMMPS.
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The *group2ndx* command will write group definitions to an index file.
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Without specifying any group IDs, all groups will be written to the
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index file. When specifying group IDs, only those groups will be
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written to the index file. In order to follow the Gromacs conventions,
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the group *all* will be renamed to *System* in the index file.
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The *ndx2group* command will create or update group definitions from
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those stored in an index file. Without specifying any group IDs, all
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groups except *System* will be read from the index file and the
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corresponding groups recreated. If a group of the same name already
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exists, it will be completely reset. When specifying group IDs, those
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groups, if present, will be read from the index file and restored.
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File Format
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"""""""""""
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The file format is equivalent and compatible with what is produced by
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the `Gromacs make_ndx command <https://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_.
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and follows the `Gromacs definition of an ndx file <https://manual.gromacs.org/current/reference-manual/file-formats.html#ndx>`_
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Each group definition begins with the group name in square brackets with
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blanks, e.g. \[ water \] and is then followed by the list of atom
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indices, which may be spread over multiple lines. Here is a small
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example file:
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.. code-block:: ini
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[ Oxygen ]
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1 4 7
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[ Hydrogen ]
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2 3 5 6
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8 9
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[ Water ]
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1 2 3 4 5 6 7 8 9
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The index file defines 3 groups: Oxygen, Hydrogen, and Water and the
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latter happens to be the union of the first two.
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----------
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Restrictions
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""""""""""""
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These commands require that atoms have atom IDs, since this is the
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information that is written to the index file.
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These commands are part of the EXTRA-COMMAND package. They are only
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enabled if LAMMPS was built with that package. See the
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:doc:`Build package <Build_package>` page for more info.
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Related commands
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""""""""""""""""
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:doc:`group <group>`, :doc:`dump <dump>`, :doc:`fix colvars <fix_colvars>`
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Default
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"""""""
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none
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