GMX-BUNDLE(1)

💖 GMX-BUNDLE 💖

okay so bestie, you're looking at gmx-bundle — that's a GROMACS manual page, and I'm about to make it make sense. axes, helices, kinks, the whole vibe. let's go 👑

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✨ NAME ✨

gmx-bundle — analyze bundles of axes, e.g., helices

✨ SYNOPSIS ✨

gmx bundle [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
           [-ol [<.xvg>]] [-od [<.xvg>]] [-oz [<.xvg>]]
           [-ot [<.xvg>]] [-otr [<.xvg>]] [-otl [<.xvg>]]
           [-ok [<.xvg>]] [-okr [<.xvg>]] [-okl [<.xvg>]]
           [-oa [<.pdb>]] [-b <time>] [-e <time>] [-dt <time>]
           [-tu <enum>] [-xvg <enum>] [-na <int>] [-[no]z]

✨ DESCRIPTION ✨

okay so gmx bundle analyzes bundles of axes. and bestie, "axes" here can be literally whatever axes you want — helix axes are the classic example, but we're not gatekeeping 🔥

here's the tea: the program reads two index groups and divides both of them into -na parts. the centers of mass of those parts are what define the tops and bottoms of the axes. like, that's the whole anatomy of an axis right there.

then several quantities get written to file — and here's the full list, no skips:

• the axis length
• the distance of the axis mid-points with respect to the average center of all axes
• the z-shift of the axis mid-points with respect to the average center of all axes
• the total tilt
• the radial tilt
• the lateral tilt

(the tilts are all measured with respect to the average axis, for the record 💅)

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with options -ok, -okr and -okl, you get the total, radial and lateral kinks of the axes plotted. iconic. but heads up bestie: this needs an extra index group of kink atoms, and that group also gets divided into -na parts. the kink angle is defined as the angle between the kink-top and the bottom-kink vectors. that's the definition, no notes.

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and with option -oa? the top, mid (or kink when -ok is set 🌸) and bottom points of each axis get written to a .pdb file each frame. the residue numbers correspond to the axis numbers. cute, right?

💡 pro tip from the manual, verbatim vibes: when viewing this file with Rasmol, use the command line option -nmrpdb, and type set axis true to display the reference axis. periodt.

✨ OPTIONS ✨

🌸 options to specify input files 🌸

• -f [<.xtc/.trr/...>] (traj.xtc) — the 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) — the index file

🎀 options to specify output files 🎀

• -ol [<.xvg>] (bun_len.xvg) — xvgr/xmgr file
• -od [<.xvg>] (bun_dist.xvg) — xvgr/xmgr file
• -oz [<.xvg>] (bun_z.xvg) — xvgr/xmgr file
• -ot [<.xvg>] (bun_tilt.xvg) — xvgr/xmgr file
• -otr [<.xvg>] (bun_tiltr.xvg) — xvgr/xmgr file
• -otl [<.xvg>] (bun_tiltl.xvg) — xvgr/xmgr file
• -ok [<.xvg>] (bun_kink.xvg) (Optional) — xvgr/xmgr file
• -okr [<.xvg>] (bun_kinkr.xvg) (Optional) — xvgr/xmgr file
• -okl [<.xvg>] (bun_kinkl.xvg) (Optional) — xvgr/xmgr file
• -oa [<.pdb>] (axes.pdb) (Optional) — protein data bank 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)
• -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -na <int> (0) — number of axes
• -[no]z (no) — use the z-axis as reference instead of the average axis

✨ SEE ALSO ✨

gmx(1)

more info about GROMACS is available at http://www.gromacs.org/ 🦋

✨ COPYRIGHT ✨

2026, GROMACS development team

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and that's the whole page bestie, you ate it 💅✨ this was GROMACS 2026.4, dated Oct 02, 2026 — go forth and bundle those axes, ily 🫶🎀