gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]] [-natoms <int>] [-[no]twin]
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 boolean operations, you can split groups into chains, residues or atoms. You can delete and rename groups. Type ‘h’ in the editor for more details.
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.
See also gmx select -on, which provides an alternative way for constructing index groups. It covers nearly all of gmx make_ndx functionality, and in many cases much more.
Options to specify input files:
- -f [<.gro/.g96/…>] (conf.gro) (Optional)
Structure file: gro g96 pdb brk ent esp tpr
- -n [<.ndx> […]] (index.ndx) (Optional)
Options to specify output files:
- -o [<.ndx>] (index.ndx)
- -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
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2020, GROMACS development team