GMX-NMTRAJ(1)

✨ gmx-nmtraj 💫

okay bestie, welcome to your new fave page in the GROMACS manual (that's the gmx-nmtraj(1) one, section 1, we're fancy like that 💅).

🌸 NAME 🌸

gmx-nmtraj — makes a virtual wiggling trajectory out of an eigenvector, fr fr.

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🎀 SYNOPSIS 🎀

gmx nmtraj [-s [<.tpr/.gro/...>]] [-v [<.trr/.cpt/...>]]
           [-o [<.xtc/.trr/...>]] [-eignr <string>]
           [-phases <string>] [-temp <real>] [-amplitude <real>]
           [-nframes <int>]

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🦋 DESCRIPTION 🦋

so, gmx-nmtraj generates a virtual trajectory from an eigenvector — think of it as a harmonic Cartesian oscillation doing its little dance around the average structure 🩰. It's giving "vibe check but with physics."

Those eigenvectors? They should normally be mass-weighted, but you can use non-weighted eigenvectors to generate orthogonal motions instead. iykyk.

The output frames get written as a trajectory file that covers one entire period, and the very first frame is the average structure. ✨ And listen — if you write that trajectory in (or convert it to) PDB format, you can view it directly in PyMol and even render a full-on photorealistic movie 👑🎬. yes bestie, movie star behavior.

Motion amplitudes are calculated from the eigenvalues and a preset temperature, assuming equipartition of the energy over all modes. To make the motion clearly visible in PyMol you might want to amplify it by setting an unrealistically high temperature 🙈... but bestie, be aware: both the linear Cartesian displacements and the mass weighting will lead to serious structure deformation for high amplitudes. It's simply a limitation of the Cartesian normal mode model, no cap. 💀

By default the selected eigenvector is set to 7, since the first six normal modes are the translational and rotational degrees of freedom. (yes, those are the ones we skip, periodt.)

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🔥 OPTIONS 🔥

💖 Options to specify input files:

• -s [<.tpr/.gro/...>] (topol.tpr) — Structure+mass(db). Formats: tpr gro g96 pdb brk ent
• -v [<.trr/.cpt/...>] (eigenvec.trr) — Full precision trajectory. Formats: trr cpt tng h5md

🎀 Options to specify output files:

• -o [<.xtc/.trr/...>] (nmtraj.xtc) — Trajectory. Formats: xtc trr gro g96 pdb tng h5md

⭐ Other options:

• -eignr <string> (7) — String of eigenvectors to use, where the first one is 1. 👑
• -phases <string> (0.0) — String of phases (the default is 0.0, cute).
• -temp <real> (300) — Temperature, in K 🌡️
• -amplitude <real> (0.25) — Amplitude for modes with eigenvalue <=0
• -nframes <int> (30) — Number of frames to generate 🌈

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👑 SEE ALSO 👑

gmx(1)

More info about GROMACS is hanging out at <‐ http://www.gromacs.org/> — go look, bestie 🫶

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💜 COPYRIGHT 💜

2026, GROMACS development team

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no thoughts, just oscillating 💫 k bye, go render that movie Ctrl+C-free 🍓

stay iconic, this was GMX-NMTRAJ(1) from the GROMACS manual, version 2026.4, dated Oct 02, 2026 🧚✨