GMX-RMSDIST(1)

🎀 NAME 🎀

gmx-rmsdist — the gmx subcommand that calculates atom pair distances averaged with power -2, -3 or -6 💅

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✨ SYNOPSIS ✨

gmx rmsdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-equiv [<.dat>]] [-o [<.xvg>]] [-rms [<.xpm>]]
            [-scl [<.xpm>]] [-mean [<.xpm>]] [-nmr3 [<.xpm>]]
            [-nmr6 [<.xpm>]] [-noe [<.dat>]] [-b <time>] [-e <time>]
            [-dt <time>] [-[no]w] [-xvg <enum>] [-nlevels <int>]
            [-max <real>] [-[no]sumh] [-[no]pbc]

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🦋 DESCRIPTION 🦋

okay so bestie, listen up. gmx rmsdist computes the root mean square deviation of atom distances, and the iconic part is that no fit is needed — unlike in the standard RMS deviation that gmx rms computes. The reference structure just gets taken straight from the structure file. The RMSD at time t is calculated as the RMS of the differences in distance between atom-pairs in the reference structure and the structure at time t. like, it's giving distance-truthing, fr fr. 💖

gmx rmsdist can also produce matrices of the rms distances, rms distances scaled with the mean distance and the mean distances, plus matrices with NMR averaged distances (that's 1/r^3 and 1/r^6 averaging, no cap). And finally, lists of atom pairs with 1/r^3 and 1/r^6 averaged distance below the maximum distance (-max, which will default to 0.6 in this case) can be generated, by default averaging over equivalent hydrogens (all triplets of hydrogens named *[123]). Additionally a list of equivalent atoms can be supplied (-equiv), each line containing a set of equivalent atoms specified as residue number and name and atom name; e.g.:

HB* 3 SER  HB1 3 SER  HB2

⚠️ Residue and atom names must exactly match those in the structure file, including case. Specifying non-sequential atoms is undefined. 🙈 so like, don't be sloppy with the spelling or the whole vibe check fails.

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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
• -equiv [<.dat>] (equiv.dat) (Optional) — Generic data file

💜 Options to specify output files 💜

• -o [<.xvg>] (distrmsd.xvg) — xvgr/xmgr file
• -rms [<.xpm>] (rmsdist.xpm) (Optional) — X PixMap compatible matrix file
• -scl [<.xpm>] (rmsscale.xpm) (Optional) — X PixMap compatible matrix file
• -mean [<.xpm>] (rmsmean.xpm) (Optional) — X PixMap compatible matrix file
• -nmr3 [<.xpm>] (nmr3.xpm) (Optional) — X PixMap compatible matrix file
• -nmr6 [<.xpm>] (nmr6.xpm) (Optional) — X PixMap compatible matrix file
• -noe [<.dat>] (noe.dat) (Optional) — Generic data 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
• -nlevels <int> (40) — Discretize RMS in this number of levels
• -max <real> (-1) — Maximum level in matrices
• -[no]sumh (yes) — Average distance over equivalent hydrogens
• -[no]pbc (yes) — Use periodic boundary conditions when computing distances

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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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and that's the whole page bestie, periodt ✨ this was GROMACS version 2026.4, dated Oct 02, 2026 — go read your trajectories and slay 💅🌈