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gmx make_ndx |
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Main Table of Contents | VERSION 5.0-20140629-b0f0873-dirty-unknown |
gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]] [-nice] [-natoms ] [-[no]twin]
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.