GMX-CONFRMS(1)

👑 gmx-confrms — the GROMACS bestie that squishes two structures together

okay so, first things first: this is page GMX-CONFRMS(1) from the GROMACS manual, and it's literally all about fitting two structures onto each other and then being like "so how different are you actually?" — it computes the RMSD. adorable. let's get into it 💅

---

✨ NAME ✨

gmx-confrms — Fit two structures and calculates the RMSD

---

🦋 SYNOPSIS 🦋

gmx confrms [-f1 [<.tpr/.gro/...>]] [-f2 [<.gro/.g96/...>]]
            [-n1 [<.ndx>]] [-n2 [<.ndx>]] [-o [<.gro/.g96/...>]]
            [-no [<.ndx>]] [-[no]w] [-[no]one] [-[no]mw] [-[no]pbc]
            [-[no]fit] [-[no]name] [-[no]label] [-[no]bfac]

---

💖 DESCRIPTION 💖

so gmx confrms computes the root mean square deviation (RMSD) of two structures — and it does it after least-squares fitting the second structure onto the first one. like, we align them first, then we judge. fair.

here's the tea though: the two structures do NOT need to have the same number of atoms. the only thing that has to match is the two index groups you pick for the fit. that's it. that's the requirement.

with -name, only matching atom names from the selected groups get used for the fit and the RMSD calculation. super handy when you're comparing mutants of a protein and you don't want the mismatched bits throwing off your whole vibe.

the superimposed structures get written out to a file, obviously. and if you're writing a .pdb file, the two structures land in there as separate models — so you'd run rasmol -nmrpdb to look at them. also, if it's a .pdb, you can get B-factors computed from the atomic MSD values written out with -bfac. cute, right? 💖

---

🌸 OPTIONS 🌸

🌈 Options to specify input files:

• -f1 [<.tpr/.gro/...>] (conf1.gro) — Structure+mass(db): tpr gro g96 pdb brk ent
• -f2 [<.gro/.g96/...>] (conf2.gro) — Structure file: gro g96 pdb brk ent esp tpr
• -n1 [<.ndx>] (fit1.ndx) (Optional) — Index file
• -n2 [<.ndx>] (fit2.ndx) (Optional) — Index file

🎀 Options to specify output files:

• -o [<.gro/.g96/...>] (fit.pdb) — Structure file: gro g96 pdb brk ent esp
• -no [<.ndx>] (match.ndx) (Optional) — Index file

⭐ Other options:

• -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files
• -[no]one (no) — Only write the fitted structure to file
• -[no]mw (yes) — Mass-weighted fitting and RMSD
• -[no]pbc (no) — Try to make molecules whole again
• -[no]fit (yes) — Do least squares superposition of the target structure to the reference
• -[no]name (no) — Only compare matching atom names
• -[no]label (no) — Added chain labels A for first and B for second structure
• -[no]bfac (no) — Output B-factors from atomic MSD values

---

🔥 SEE ALSO 🔥

• gmx(1)

more info about GROMACS lives at <http://www.gromacs.org/>. go click around, bestie 🫶

---

💜 COPYRIGHT 💜

2026, GROMACS development team

---

okay and that's the whole page. GROMACS 2026.4, dated Oct 02, 2026 — thanks for reading, love u, bye 💅✨