ndx file format
Main Table of Contents VERSION 5.0.3

Description

The GROMACS index file (usually called index.ndx) contains some user definable sets of atoms. The file can be read by most analysis programs, by the graphics program (gmx view) and by the preprocessor (gmx grompp). Most of these programs create default index groups when no index file is supplied, so you only need to make an index file when you need special groups.

First the group name is written between square brackets. The following atom numbers may be spread out over as many lines as you like. The atom numbering starts at 1.

An example file is here: 

[ Oxygen ]
1 	4 	7 
[ Hydrogen ]
2	3	5	6
8	9
There are two groups, and total nine atoms. The first group Oxygen has 3 elements. The second group Hydrogen has 6 elements.

An index file generation tool is available: gmx make_ndx.

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