GMX-HELIX(1)

🎀 NAME 🎀

gmx-helix — okay so bestie, this is the GROMACS tool that calculates basic properties of alpha helices. That's it, that's the whole job, and it does it so well. Manual section 1, for the record. 💖

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✨ SYNOPSIS ✨

gmx helix [-s [<.tpr>]] [-n [<.ndx>]] [-f [<.xtc/.trr/...>]]
          [-cz [<.gro/.g96/...>]] [-b <time>] [-e <time>]
          [-dt <time>] [-[no]w] [-r0 <int>] [-[no]q] [-[no]F]
          [-[no]db] [-[no]ev] [-ahxstart <int>] [-ahxend <int>]

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🦋 DESCRIPTION 🦋

Okay so here's the tea: gmx helix computes all kinds of helix properties. Literally all of them. It's giving full coverage. 👑

First things first — the peptide gets checked to find the longest helical part, and how does it decide? By hydrogen bonds and phi/psi angles, obviously. Then that bit gets fitted to an ideal helix, spun around the z-axis, and centered around the origin. Origin main character energy fr fr. ✨

And then, the following properties get computed:

• Helix radius (file radius.xvg). This is merely the RMS deviation in two dimensions for all Calpha atoms. It is calculated as sqrt((sum_i (x^2(i)+y^2(i)))/N) where N is the number of backbone atoms. For an ideal helix the radius is 0.23 nm. 💫
• Twist (file twist.xvg). The average helical angle per residue gets calculated. For an alpha-helix it is 100 degrees, for 3-10 helices it will be smaller, and for 5-helices it will be larger. The way it just scales like that… iconic.
• Rise per residue (file rise.xvg). The helical rise per residue is plotted as the difference in z-coordinate between Calpha atoms. For an ideal helix, this is 0.15 nm. 🌸
• Total helix length (file len-ahx.xvg). The total length of the helix in nm. This is simply the average rise (see above) times the number of helical residues (see below). Simple math, slay.
• Helix dipole, backbone only (file dip-ahx.xvg). No side chains invited to this party. 🎀
• RMS deviation from ideal helix, calculated for the Calpha atoms only (file rms-ahx.xvg). Just the Calphas. Sorry to everyone else.
• Average Calpha - Calpha dihedral angle (file phi-ahx.xvg).
• Average phi and psi angles (file phipsi.xvg). The classic duo. 💅
• Ellipticity at 222 nm according to Hirst and Brooks. Yup, named after actual people.

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🌈 OPTIONS 🌈

💜 Options to specify input files: 💜

• -s [<.tpr>] (topol.tpr) — Portable xdr run input file. Your whole topology situation goes here.
• -n [<.ndx>] (index.ndx) — Index file. Group definitions, bestie, groups.
• -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory. And the formats it'll take are: xtc trr cpt gro g96 pdb tng h5md. So many options, we love a flexible queen. ✨

🩷 Options to specify output files: 🩷

• -cz [<.gro/.g96/...>] (zconf.gro) — Structure file. Formats: gro g96 pdb brk ent esp.

🧚 Other options: 🧚

• -b <time> (0) — Time of first frame to read from trajectory (default unit ps).
• -e <time> (0) — Time of last frame to read from trajectory (default unit ps).
• -dt <time> (0) — Only use frame when t MOD dt = first time (default unit ps). Do the math, it's fine. 💀
• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files. Turning this on pops the plots right up in front of you.
• -r0 <int> (1) — The first residue number in the sequence.
• -[no]q (no) — Check at every step which part of the sequence is helical. Every. Single. Step. Obsessed.
• -[no]F (yes) — Toggle fit to a perfect helix. It's yes by default, so the fit is already on unless you say otherwise.
• -[no]db (no) — Print debug info. For when you simply must know what's happening internally. 🙈
• -[no]ev (no) — Write a new 'trajectory' file for ED.
• -ahxstart <int> (0) — First residue in helix.
• -ahxend <int> (0) — Last residue in helix.

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💫 SEE ALSO 💫

• gmx(1) — the mothership, go say hi.

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

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👑 COPYRIGHT 👑

2026, GROMACS development team

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Ate and left no crumbs, fr fr. That's the whole page. Go fit some helices. 💖✨

GROMACS 2026.4 🌸 dated Oct 02, 2026 🦋 — mwah, love u, bye bestie! 💅🎀