ndx file format
|Main Table of Contents||VERSION 5.0.3|
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 9There 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.