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group2ndx command

ndx2group command

Syntax

group2ndx file args
ndx2group file args

  • file = name of index file to write out or read in

  • args = zero or more group IDs may be appended

Examples

group2ndx allindex.ndx
group2ndx someindex.ndx upper lower mobile
ndx2group someindex.ndx
ndx2group someindex.ndx mobile

Description

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 used with in combination with Gromacs analysis tools or to import group definitions into the fix colvars input file.

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. Without specifying any group IDs, all groups will be written to the index file. When specifying group IDs, only those groups will be written to the index file. In order to follow the Gromacs conventions, the group all will be renamed to System in the index file.

The ndx2group command will create or update group definitions from those stored in an index file. Without specifying any group IDs, all groups except System will be read from the index file and the corresponding groups recreated. If a group of the same name already exists, it will be completely reset. When specifying group IDs, those 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. and follows the Gromacs definition of an ndx file

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:

[ 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.

Restrictions

These commands require that atoms have atom IDs, since this is the information that is written to the index file.

These commands are part of the EXTRA-COMMAND package. They are only enabled if LAMMPS was built with that package. See the Build package page for more info.

Default

none