group2ndx command

ndx2group command

Syntax

group2ndx file group-ID ...
ndx2group file group-ID ...
  • file = name of index file to write out or read in
  • 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.

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 of 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.


Restrictions

This command requires that atoms have atom IDs, since this is the information that is written to the index file.

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