Provided by: gromacs-data_2018.1-1_all 
NAME
gmx-make_ndx - Make index files
SYNOPSIS
gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]]
[-natoms <int>] [-[no]twin]
DESCRIPTION
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
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)
Index file
Options to specify output files:
-o [<.ndx>] (index.ndx)
Index file
Other options:
-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
SEE ALSO
gmx(1) More information about GROMACS is available at <http://www.gromacs.org/>.
COPYRIGHT
2018, GROMACS development team