Section: GROMACS suite, VERSION 4.5 (1)Updated: Thu 26 Aug 2010Local indexUp
make_ndx - makes index files
make_ndx-f conf.gro -n index.ndx -o index.ndx -[no]h-[no]version-nice int -natoms int
Index groups are necessary for almost every gromacs program.
All these programs can generate default index groups. You ONLY
have to use make_ndx when you need SPECIAL index groups.
There is a default index group for the whole system, 9 default
index groups are generated for proteins, a default index group
is generated for every other residue name.
When no index file is supplied, also make_ndx will generate the
With the index editor you can select on atom, residue and chain names
When a run input file is supplied you can also select on atom type.
You can use NOT, AND and OR, you can split groups
into chains, residues or atoms. You can delete and rename groups.
The atom numbering in the editor and the index file starts at 1.
-f conf.groInput, Opt. Structure file: gro g96 pdb tpr etc.
-n index.ndxInput, Opt., Mult. Index file
-o index.ndxOutput Index file
-[no]hno Print help info and quit
-[no]versionno Print version info and quit
-nice int 0 Set the nicelevel
-natoms int 0 set number of atoms (default: read from coordinate or index file)