GMX-HELIXORIENT(1)

✨ GMX-HELIXORIENT(1) ✨ — the GROMACS one 🌀💖

okay bestie, welcome to gmx-helixorient, a lil tool from the GROMACS fam that literally reads the vibes of your alpha helices 💅

🎀 NAME 🎀

gmx-helixorient — calculate local pitch/bending/rotation/orientation inside helices 🌀✨

📜 SYNOPSIS 📜

gmx helixorient [-s [<.tpr>]] [-f [<.xtc/.trr/...>]] [-n [<.ndx>]]
             [-oaxis [<.dat>]] [-ocenter [<.dat>]] [-orise [<.xvg>]]
             [-oradius [<.xvg>]] [-otwist [<.xvg>]]
             [-obending [<.xvg>]] [-otilt [<.xvg>]] [-orot [<.xvg>]]
             [-b <time>] [-e <time>] [-dt <time>] [-xvg <enum>]
             [-[no]sidechain] [-[no]incremental]

💫 DESCRIPTION 💫

so gmx helixorient goes in and calculates the coordinates and direction of the average axis inside an alpha helix, plus the direction/vectors of BOTH the Calpha and (if you want, queen) a sidechain atom relative to that axis. it's giving geometry, it's giving structure analysis, it's giving main character energy 🫶

for input, you gotta hand it an index group with Calpha atoms that correspond to an alpha-helix of continuous residues. no random gaps bestie, we said continuous. 🌸

and for the sidechain directions? you need a second index group — same size as the first — containing the heavy atom in each residue that should represent the sidechain. same size. SAME SIZE. ✨

⚠️ heads up: this program does not do any fitting of structures. no fitting. none. zero. not a thing it does. 💀

also we need four Calpha coordinates to define the local direction of the helix axis. four. that's the whole requirement. iconic. 🍓

okay now the cute part, the math ✨ the tilt/rotation is calculated from Euler rotations, where we define:

• the helix axis as the local x-axis
• the residues/Calpha vector as y
• and the z-axis from their cross product 🧚

we use the Euler Y-Z-X rotation, which means we first tilt the helix axis:

1. around the residues vector, and
2. orthogonal to the residues vector,

...and finally apply the (3) rotation around it. and because we're thorough like that, for debugging or other purposes we ALSO write out the actual Euler rotation angles as theta[1-3].xvg 💅 slay.

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🌈 OPTIONS 🌈

📥 Options to specify input files

• -s [<.tpr>] (topol.tpr) — portable xdr run input file 🧬
• -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory, bestie: xtc trr cpt gro g96 pdb tng h5md 🎞️
• -n [<.ndx>] (index.ndx) — index file ✨ (optional, no pressure)

📤 Options to specify output files

• -oaxis [<.dat>] (helixaxis.dat) — generic data file 🌀
• -ocenter [<.dat>] (center.dat) — generic data file 📍
• -orise [<.xvg>] (rise.xvg) — xvgr/xmgr file 📈
• -oradius [<.xvg>] (radius.xvg) — xvgr/xmgr file ⭕
• -otwist [<.xvg>] (twist.xvg) — xvgr/xmgr file 🍥
• -obending [<.xvg>] (bending.xvg) — xvgr/xmgr file 〰️
• -otilt [<.xvg>] (tilt.xvg) — xvgr/xmgr file 📐
• -orot [<.xvg>] (rotation.xvg) — xvgr/xmgr file 🔄

🎛️ 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) ⏱️
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none 🎨
• -[no]sidechain (no) — calculate sidechain directions relative to helix axis too 🌿
• -[no]incremental (no) — calculate incremental rather than total rotation/tilt 📊

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👀 SEE ALSO 👀

• gmx(1) 🫶

more info about GROMACS is available at <http://www.gromacs.org/> — go look, bestie, it's right there 🌐

©️ COPYRIGHT ©️

2026, GROMACS development team 💜

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and that's the whole page, angel 🎀 version 2026.4, dated Oct 02, 2026 — go analyze those helices, they're gonna eat 💅✨