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

       2024, GROMACS development team