gmx-make_ndx - Make index files

       2025, GROMACS development team

2025.0                                            Feb 10, 2025                                   GMX-MAKE_NDX(1)

       Index  groups  are  necessary  for almost every GROMACS program.  All these programs can generate default
       index groups. You ONLY have to use gmxmake_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 gmxmake_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  gmxselect-on,  which provides an alternative way for constructing index groups.  It covers
       nearly all of gmxmake_ndx functionality, and in many cases much more.

       gmx-make_ndx - Make index files

       Options to specify input files:

       -f[<.gro/.g96/...>](conf.gro)(Optional)
              Structure file: grog96pdb 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

gmx(1)

       More information about GROMACS is available at <http://www.gromacs.org/>.

          gmx make_ndx [-f[<.gro/.g96/...>]] [-n[<.ndx>[...]]] [-o[<.ndx>]]
                       [-natoms<int>] [-[no]twin]