GMX-RMSF(1)

💖 GMX-RMSF(1) — the gmx rmsf page, bestie edition 💖

okay so. this is the manual page for gmx-rmsf, aka gmx rmsf, from the GROMACS suite (that's the manual this page lives in, mwah). it's the one that calculates atomic fluctuations. yes, the wiggly stuff. the "how much does this atom vibe-shift around its average position" stuff. iconic behavior honestly. 🦋

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✨ NAME ✨

gmx-rmsf — calculate atomic fluctuations 💅

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✨ SYNOPSIS ✨

gmx rmsf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
         [-q [<.pdb>]] [-oq [<.pdb>]] [-ox [<.pdb>]] [-o [<.xvg>]]
         [-od [<.xvg>]] [-oc [<.xvg>]] [-dir [<.log>]] [-b <time>]
         [-e <time>] [-dt <time>] [-[no]w] [-xvg <enum>] [-[no]res]
         [-[no]aniso] [-[no]fit]

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✨ DESCRIPTION ✨

so gmx rmsf computes the root mean square fluctuation — RMSF, which is literally just the standard deviation, no cap — of atomic positions in the trajectory. that trajectory comes in through -f.

and before it does all that, it optionally fits to a reference frame, which you supply with -s. cute, right?

with the -oq option, the RMSF values get converted into B-factor values, and those get written out to a .pdb file. by default, the coordinates in that output file are taken from the structure file you gave it with -s — although you can instead use coordinates read from a different .pdb file, provided with -q. 🎀

⚠️ okay real talk for a sec: there is very little error checking here. so in this case, it is your responsibility to make sure all atoms in the structure file and the .pdb file correspond exactly to each other. exactly. like, no wiggle room. you've been warned bestie 😭

the -ox option writes the B-factors to a file together with the average coordinates in the trajectory.

and with the -od option, the root mean square deviation with respect to the reference structure gets calculated. different thing! similar-ish name! don't mix them up 💀

with the -aniso option, gmx rmsf will compute anisotropic temperature factors, and then it will also output average coordinates and a .pdb file with ANISOU records (that corresponds to the -oq or -ox option). 📝

⚠️ please note that the U values are orientation-dependent, so before you go comparing anything with experimental data, you should verify that you fit to the experimental coordinates. seriously. verify. 🌸

when a .pdb input file is passed to the program and the -aniso flag is set, a correlation plot of the Uij will be created — but only if any anisotropic temperature factors are present in the .pdb file. conditional queen 👑

with the -dir option, the average MSF (3x3) matrix gets diagonalized. this shows you the directions in which the atoms fluctuate the most and the least. main character directions, honestly 🔥

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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
• -q [<.pdb>] (eiwit.pdb) (Optional) — Protein data bank file

🦋 options to specify output files:

• -oq [<.pdb>] (bfac.pdb) (Optional) — Protein data bank file
• -ox [<.pdb>] (xaver.pdb) (Optional) — Protein data bank file
• -o [<.xvg>] (rmsf.xvg) — xvgr/xmgr file
• -od [<.xvg>] (rmsdev.xvg) (Optional) — xvgr/xmgr file
• -oc [<.xvg>] (correl.xvg) (Optional) — xvgr/xmgr file
• -dir [<.log>] (rmsf.log) (Optional) — Log file

💜 other options:

• -b <time> (0) — time of first frame to read from the trajectory (default unit is ps)
• -e <time> (0) — time of 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)
• -[no]w (no) — view output .xvg, .xpm, .eps and .pdb files
• -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
• -[no]res (no) — calculate averages for each residue
• -[no]aniso (no) — compute anisotropic temperature factors
• -[no]fit (yes) — do a least squares superposition before computing RMSF. without this, you must make sure that the reference structure and the trajectory match 😤

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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 🫶 this was GROMACS 2026.4, dated Oct 02, 2026 — go forth and fluctuate responsibly, you absolute icon 👑✨