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GMX-MAKE_NDX(1)			    GROMACS		       GMX-MAKE_NDX(1)

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 de-
       fault 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 aha 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 mem-
       brane setups.

       See also	gmx select -on,	which provides an  alternative	way  for  con-
       structing index groups.	It covers nearly all of	gmx make_ndx function-
       ality, and in many cases	much more.

OPTIONS
       Options to specify input	files:

       -f [<.gro/.g96/^a|>] (conf.gro) (Optional)
	      Structure	file: gro g96 pdb brk ent esp tpr

       -n [<.ndx> [^a|]]	(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
       2020, GROMACS development team

2020.3				 Jul 09, 2020		       GMX-MAKE_NDX(1)

NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT

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