GMX-MAKE_NDX(1)

✨ GMX-MAKE_NDX ✨

okay bestie so this is gmx-make_ndx, aka the GROMACS index file maker, and it's genuinely one of my faves 🎀

🌸 SYNOPSIS 🌸

gmx make_ndx [-f [<.gro/.g96/...>]] [-n [<.ndx> [...]]] [-o [<.ndx>]]
             [-natoms <int>] [-[no]twin]

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💖 DESCRIPTION 💖

So like, index groups? Necessary. For almost every single GROMACS program. That's not me being dramatic, that's just the truth 💅

But here's the tea: all those programs can generate default index groups on their own. You ONLY have to reach for gmx make_ndx when you need SPECIAL index groups. Like, custom ones. Yours. Main character groups ✨

And the defaults are already pretty generous, ngl:

• there's a default index group for the whole system
• there are 9 default index groups for proteins
• and a default index group gets generated for every other residue name

When no index file is supplied, gmx make_ndx will also generate the default groups. No thoughts, just defaults 🫶

With the index editor you can select on atom, residue and chain names and numbers. And when a run input file is supplied you can also select on atom type. Obsessed.

You can use boolean operations, you can split groups into chains, residues or atoms. You can delete and rename groups. Type h in the editor for more details — she's got lore, ask her 📖

Also super important: the atom numbering in the editor and the index file starts at 1. Not 0. One. Got it bestie? 😭

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

See also gmx select -on, which provides an alternative way for constructing index groups. It covers nearly all of gmx make_ndx functionality, and in many cases much more. So like… yes, we have options 💀

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🎀 OPTIONS 🎀

🦋 Options to specify input files:

• -f [<.gro/.g96/...>] (conf.gro) (Optional) — structure file, and she accepts: 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, and yes she'll make you a new one

⭐ 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

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💜 SEE ALSO 💜

• gmx(1)

More information about GROMACS is available at <http://www.gromacs.org/>.

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👑 COPYRIGHT 👑

2026, GROMACS development team

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okay that's the whole page, you ate that 💖 this was 2026.4, dated Oct 02, 2026, and that's the vibe check, periodt 🎀✨🦋