GMX-GYRATE(1)

🦋 GMX-GYRATE — it's givin' radius of gyration 💫

okay bestie, welcome to the GROMACS corner of the manual, page gmx-gyrate. Yes it's the new one. Yes it slays. Let's go 🫶

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✨ NAME ✨

gmx-gyrate — Calculate radius of gyration of a molecule

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🎀 SYNOPSIS 🎀

gmx gyrate [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
           [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
           [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
           [-[no]rmpbc] [-sf <file>] [-selrpos <enum>]
           [-seltype <enum>] [-sel <selection>] [-mode <enum>]

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🌸 DESCRIPTION 🌸

So. gmx gyrate computes the radius of gyration of a molecule, plus the radii of gyration about the x-, y- and z-axes, as a function of time. And the atoms are explicitly mass weighted, no cap, that's just how it is 💅

The axis components correspond to the mass-weighted root-mean-square of the radii components orthogonal to each axis, for example:

Rg(x) = sqrt((sum_i w_i (R_i(y)^2 + R_i(z)^2))/(sum_i w_i)).

where w_i is the weight value in the given situation (mass, charge, unit)

🚨 okay important thing bestie: this is a new implementation of the gyrate utility added in GROMACS 2024. If you need the old one, use gmx gyrate-legacy. Don't come for me, come for legacy 💀

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✨ OPTIONS ✨

📥 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — Input structure: tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) (Optional) — Extra index groups

📤 Options to specify output files:

• -o [<.xvg>] (gyrate-taf.xvg) — Filename for gyrate plot output

🌈 Other options:

• -b <time> (0) — First frame (ps) to read from trajectory
• -e <time> (0) — Last frame (ps) to read from trajectory
• -dt <time> (0) — Only use frame if t MOD dt == first time (ps)
• -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s
• -fgroup <selection> — Atoms stored in the trajectory file (if not set, assume first N atoms)
• -xvg <enum> (xmgrace) — Plot formatting: xmgrace, xmgr, none
• -[no]rmpbc (yes) — Make molecules whole for each frame
• -sf <file> — Provide selections from files
• -selrpos <enum> (atom) — Selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
• -seltype <enum> (atom) — Default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
• -sel <selection> — Select group to compute gyrate radius
• -mode <enum> (mass) — Atom weighting mode: mass, charge, geometry

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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

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k that's the whole thing, you ate that fr fr 🍓 go compute some radii bestie, the vibes are immaculate. this was page gmx-gyrate from the GROMACS manual, version 2026.4, dated Oct 02, 2026 💜 iykyk 🧚