GMX-NMENS(1)

✨ GMX-NMENS(1) ✨

okay bestie, welcome to the gmx-nmens page 💖 it's a GROMACS manual page, it's giving "normal modes go brrr", and i'm gonna walk you through every single bit of it, no skips, no skimming, periodt.

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🌸 NAME 🌸

gmx-nmens — generate an ensemble of structures from the normal modes 🦋

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💅 SYNOPSIS 💅

gmx nmens [-v [<.trr/.cpt/...>]] [-e [<.xvg>]] [-s [<.tpr/.gro/...>]]
          [-n [<.ndx>]] [-o [<.xtc/.trr/...>]] [-xvg <enum>]
          [-temp <real>] [-seed <int>] [-num <int>] [-first <int>]
          [-last <int>]

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👑 DESCRIPTION 👑

so here's the tea: gmx nmens generates an ensemble around an average structure, inside a subspace that's defined by a set of normal modes (aka the eigenvectors). iconic behavior honestly.

the eigenvectors are assumed to be mass-weighted. write that down 📝

the position along each eigenvector is randomly taken from a Gaussian distribution with variance kT/eigenvalue. yes, random, yes, physics, slay.

by default the starting eigenvector is set to 7, because the first six normal modes are the translational and rotational degrees of freedom. they're busy doing their own thing, we leave them alone 🙈

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✨ OPTIONS ✨

🎀 Options to specify input files

• -v [<.trr/.cpt/...>] (eigenvec.trr) — full precision trajectory 💖 the formats it eats: trr cpt tng h5md
• -e [<.xvg>] (eigenval.xvg) — xvgr/xmgr file 📊
• -s [<.tpr/.gro/...>] (topol.tpr) — Structure+mass(db) 🧬 the formats: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) — Index file. this one's Optional, so it's giving "only if you want to" 🫶

🦋 Options to specify output files

• -o [<.xtc/.trr/...>] (ensemble.xtc) — Trajectory 🌈 the formats: xtc trr gro g96 pdb tng h5md

💜 Other options

• -xvg <enum> (xmgrace) — xvg plot formatting ✨ your choices are: xmgrace, xmgr, none
• -temp <real> (300) — Temperature in Kelvin 🌡️
• -seed <int> (0) — Random seed 🎲 (0 means generate, so it'll just make one for you, cute)
• -num <int> (100) — Number of structures to generate 💯
• -first <int> (7) — First eigenvector to use (-1 is select) 🔍
• -last <int> (-1) — Last eigenvector to use (-1 is till the last) 🏁

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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 — respect the authors bestie, they ate 🍓

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and that's the whole page, no crumbs left 💅 this was 2026.4, dated Oct 02, 2026, and it's the GMX-NMENS(1) manual, mwah 😘 go generate some ensembles, main character 🧚‍♀️✨