Provided by: gromacs-data_5.1.2-1ubuntu1_all bug

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 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.

       The -twin switch duplicates all index groups with an offset of -natoms, which is useful for Computational
       Electrophysiology double-layer membrane setups.


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
       2015, GROMACS development team

5.1.2                                           February 03, 2016                                GMX-MAKE_NDX(1)