GMX-HYDORDER(1)

💖 GMX-HYDORDER — bestie edition 💖

okay so. this is gmx-hydorder, part of the GROMACS fam 🌸. she computes tetrahedrality parameters around a given atom. that's the whole vibe. let's get into it 🫶

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✨ NAME ✨

gmx-hydorder — compute tetrahedrality parameters around a given atom 💅

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🎀 SYNOPSIS 🎀

gmx hydorder [-f [<.xtc/.trr/...>]] [-n [<.ndx>]] [-s [<.tpr>]]
             [-o [<.xpm> [...]]] [-or [<.out> [...]]]
             [-Spect [<.out> [...]]] [-b <time>] [-e <time>]
             [-dt <time>] [-[no]w] [-d <enum>] [-bw <real>]
             [-sgang1 <real>] [-sgang2 <real>] [-tblock <int>]
             [-nlevel <int>]

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🌈 DESCRIPTION 🌈

so gmx hydorder computes the tetrahedrality order parameters around a given atom. and no, she's not doing just one — both the angle order parameter and the distance order parameter get calculated. iconique. ✨

if you want the full lore, go read P.-L. Chau and A.J. Hardwick, Mol. Phys., 93, (1998), 511-518. 📚 that's where the details live. iykyk.

okay so here's the tea ☕: gmx hydorder calculates the order parameter in a 3d-mesh in the box. and if you've got 2 phases in the box, she lowkey hooks you up with the option to define a 2D interface in time separating the faces — you do that by specifying the parameters -sgang1 and -sgang2.

⚠️ bestie listen: it is important to select these judiciously. no cap. choose wisely or the whole thing is giving chaos. 😭

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💅 OPTIONS 💅

🦋 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory file, aka where your frames live. formats she eats: xtc trr cpt gro g96 pdb tng h5md 🌸
• -n [<.ndx>] (index.ndx) — the index file 👑
• -s [<.tpr>] (topol.tpr) — portable xdr run input file, the classic .tpr 💜

🍓 Options to specify output files:

• -o [<.xpm> [...]] (intf.xpm) — X PixMap compatible matrix file 🎀
• -or [<.out> [...]] (raw.out) (Optional) — generic output file
• -Spect [<.out> [...]] (intfspect.out) (Optional) — generic output file ✨

⭐ Other options:

• -b <time> (0) — time of the first frame to read from the trajectory (default unit is ps) 🕐
• -e <time> (0) — time of the last frame to read from the trajectory (default unit is ps) 🕐
• -dt <time> (0) — only use a frame when t MOD dt = first time (default unit is ps) ⏳
• -[no]w (no) — view output .xvg, .xpm, .eps and .pdb files 👀
• -d <enum> (z) — direction of the normal on the membrane. your choices: z, x, y 🧭
• -bw <real> (1) — binwidth of box mesh 📏
• -sgang1 <real> (1) — tetrahedral angle parameter in Phase 1 (bulk)
• -sgang2 <real> (1) — tetrahedral angle parameter in Phase 2 (bulk)
• -tblock <int> (1) — number of frames in one time-block average 📊
• -nlevel <int> (100) — number of Height levels in 2D - XPixMaps 📈

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👀 SEE ALSO 👀

• gmx(1)

more info about GROMACS is over at http://www.gromacs.org/ — go peek bestie 🫶

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📜 COPYRIGHT 📜

2026, GROMACS development team

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and that's the whole page, bestie!! 💖 this was GROMACS version 2026.4, dated Oct 02, 2026 — periodt. now go compute some tetrahedrality, you main character 🧚✨👑