GMX-GYRATE-LEGACY(1)

💖 gmx-gyrate-legacy — the GROMACS manual, but make it bestie 💖

okay so this is gmx-gyrate-legacy from the GROMACS fam (that's GMX-GYRATE-LEGACY(1) in the group chat, iykyk). she's here to tell you how squishy and spread out your molecule is. we love a radius-of-gyration moment. 🎀

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✨ NAME ✨

gmx-gyrate-legacy — Calculate the radius of gyration

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✨ SYNOPSIS ✨

gmx gyrate-legacy [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]]
             [-n [<.ndx>]] [-o [<.xvg>]] [-acf [<.xvg>]] [-b <time>]
             [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>]
             [-nmol <int>] [-[no]q] [-[no]p] [-[no]moi] [-nz <int>]
             [-acflen <int>] [-[no]normalize] [-P <enum>]
             [-fitfn <enum>] [-beginfit <real>] [-endfit <real>]

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✨ DESCRIPTION ✨

so bestie, gmx gyrate-legacy 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. 🦋 it's giving "how big is this thing actually" but make it science. and the atoms are explicitly mass weighted, periodt. no cap.

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 m_i (R_i(y)^2 + R_i(z)^2))/(sum_i m_i)).

and with the -nmol option, the radius of gyration gets calculated for multiple molecules by splitting the analysis group in equally sized parts. one group in, many molecules out, she's efficient like that. 💅

and with the option -nz, you get 2D radii of gyration in the x-y plane of slices along the z-axis. slicing, but make it structural. 🍓

also honorable mention: this one is the legacy version, as the name literally says. it's right there in the title. 🙈

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✨ OPTIONS ✨

🌸 Options to specify input files:

• -f [<.xtc/.trr/...>] (traj.xtc) — Trajectory: xtc trr cpt gro g96 pdb tng h5md
• -s [<.tpr/.gro/...>] (topol.tpr) — Structure+mass(db): tpr gro g96 pdb brk ent
• -n [<.ndx>] (index.ndx) (Optional) — Index file

🌈 Options to specify output files:

• -o [<.xvg>] (gyrate.xvg) — xvgr/xmgr file
• -acf [<.xvg>] (moi-acf.xvg) (Optional) — 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)
• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -nmol <int> (1) — The number of molecules to analyze
• -[no]q (no) — Use absolute value of the charge of an atom as weighting factor instead of mass
• -[no]p (no) — Calculate the radii of gyration about the principal axes.
• -[no]moi (no) — Calculate the moments of inertia (defined by the principal axes).
• -nz <int> (0) — Calculate the 2D radii of gyration of this number of slices along the z-axis
• -acflen <int> (-1) — Length of the ACF, default is half the number of frames
• -[no]normalize (yes) — Normalize ACF
• -P <enum> (0) — Order of Legendre polynomial for ACF (0 indicates none): 0, 1, 2, 3
• -fitfn <enum> (none) — Fit function: none, exp, aexp, exp_exp, exp5, exp7, exp9
• -beginfit <real> (0) — Time where to begin the exponential fit of the correlation function
• -endfit <real> (-1) — Time where to end the exponential fit of the correlation function, -1 is until the end

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✨ SEE ALSO ✨

gmx(1) — the mothership, the main character, the whole vibe. 🫶

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

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✨ COPYRIGHT ✨

2026, GROMACS development team

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and that's the whole page, bestie — no notes, she ate. 💅✨

this was GMX-GYRATE-LEGACY(1) from GROMACS, version 2026.4, dated Oct 02, 2026. go compute some radii, you icon. 🎀💖🔥