GMX-SALTBR(1)

💖 gmx-saltbr 💖 — like, the gmx-saltbr manual page, but make it make sense

okay bestie, gather round, because today we're learning about gmx-saltbr, a little GROMACS tool that literally just watches charged groups get close to each other and draws you a graph about it. it's giving chemistry gossip column, no cap. 👑

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✨ NAME ✨

gmx-saltbr — compute salt bridges 🧂🌉

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✨ SYNOPSIS ✨

gmx saltbr [-f [<.xtc/.trr/...>]] [-s [<.tpr>]] [-b <time>] [-e <time>]
           [-dt <time>] [-t <real>] [-[no]sep]

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✨ DESCRIPTION ✨

so basically 💅 — gmx saltbr plots the distance between all combination of charged groups as a function of time. yes. ALL the combinations. the groups get combined in different ways, and that's just how it is.

and here's the cute part: you can hand it a minimum distance, aka a cut-off, and any groups that are never closer than that distance simply do not get plotted. if the vibes aren't there, we're not drawing them. 🚫📉

the output goes into a bunch of fixed filenames, and they are, in order:

• min-min.xvg
• plus-min.xvg
• plus-plus.xvg

OR — plot twist 🎀 — if you turn on the -sep option, you get files for every single individual ion pair. in that case the files are named like this:

sb-(Resname)(Resnr)-(Atomnr)

⚠️ and bestie, listen to me: There may be many such files. like, MANY many. we're not joking. your directory is gonna be full. 😭

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✨ OPTIONS ✨

🦋 options to specify input files

• -f [<.xtc/.trr/...>] (traj.xtc) — the trajectory file you're feeding in. it accepts xtc trr cpt gro g96 pdb tng h5md. such a range, honestly. multi-talented icon. 🌈
• -s [<.tpr>] (topol.tpr) — the portable xdr run input file 💖

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🎀 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)
• -t <real> (1000) — the cut-off vibe check 🌸: groups that are never closer than this distance are not plotted
• -[no]sep (no) — use separate files for each interaction (may be MANY) 💀

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🔥 SEE ALSO 🔥

• gmx(1)

more info about GROMACS is available at this tiny little URL over here, it got a dash-wrap in the original so here it is fully assembled bestie: http://www.gromacs.org/ 👑

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💜 COPYRIGHT 💜

2026, GROMACS development team

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and that's the whole page, babe, you ate that 🫶 if you're ever out here drowning in sb-*.xvg files just know you chose -sep and that's on you, love you, bye 💅✨

GROMACS 2026.4 · Oct 02, 2026 · written by your girl who is literally so good at Unix 🌸