gmx-make_ndx - Make index files
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.
switch duplicates all index groups with an offset of
, 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)
- Structure file: gro g96 pdb brk ent esp tpr
- -n [<.ndx> [...]] (index.ndx)
- Index file
Options to specify output files:
- -o [<.ndx>] (index.ndx)
- Index file
- -natoms <int> (0)
- set number of atoms (default: read from coordinate or index
- -[no]twin (no)
- Duplicate all index groups with an offset of -natoms
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2017, GROMACS development team