GMX-CHECK(1)

📦
version 2026.4 · 8 versions
, in nixpkgs unstable, ubuntu stonking

💖 GMX-CHECK(1) — the gmx check page, bestie edition 💖

okay so this is GMX-CHECK(1), one of the GROMACS manual pages, and she is literally the friend who looks at your files and tells you the truth. sit down, grab a matcha, we're doing this. 🍓

✨ NAME ✨

gmx-check — check and compare files 🫶

🌈 SYNOPSIS 🌈

gmx check [-f [<.xtc/.trr/...>]] [-f2 [<.xtc/.trr/...>]] [-s1 [<.tpr>]]
          [-s2 [<.tpr>]] [-c [<.tpr/.gro/...>]] [-e [<.edr>]]
          [-e2 [<.edr>]] [-n [<.ndx>]] [-m [<.tex>]] [-vdwfac <real>]
          [-bonlo <real>] [-bonhi <real>] [-[no]rmsd] [-tol <real>]
          [-abstol <real>] [-[no]ab] [-lastener <string>]

💅 DESCRIPTION 💅

ngl, gmx check is the girl who reads your files and spills all the tea. she reads a trajectory (.tng, .trr or .xtc), an energy file (.edr), or an index file (.ndx), and prints out genuinely useful info about them. periodt. ✨

the -c option is doing the most (affectionate) — she checks whether coordinates, velocities and box are present in the file, checks for close contacts (smaller than -vdwfac and not bonded, i.e. not between -bonlo and -bonhi, all relative to the sum of both Van der Waals radii), and checks for atoms outside the box (these may occur often and are no problem, so don't panic bestie 😭). and if velocities are present, she'll calculate an estimated temperature from them. it's giving physics.

if an index file is given, its contents will be summarized. cute.

if you hand her both a trajectory and a .tpr file (with -s1), she will check whether the bond lengths defined in the tpr file are indeed correct in the trajectory. if they're not, you may have non-matching files due to e.g. deshuffling or due to problems with virtual sites. with these flags, gmx check provides a quick check for such problems. so like, a vibe check for your topology. 👑

the program can compare two run input (.tpr) files when both -s1 and -s2 are supplied. when comparing run input files this way, the default relative tolerance is reduced to 0.000001 and the absolute tolerance set to zero, to find any differences not due to minor compiler optimization differences — although you can of course still set any other tolerances through the options. similarly a pair of trajectory files can be compared (using the -f2 option), or a pair of energy files (using the -e2 option). twin energy files? compared. iconic.

for free energy simulations, the A and B state topology from one run input file can be compared with options -s1 and -ab. slay. 💖

🎀 OPTIONS 🎀

🌸 options to specify input files 🌸

  • -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — Trajectory: xtc trr cpt gro g96 pdb tng h5md
  • -f2 [<.xtc/.trr/...>] (traj.xtc) (Optional) — Trajectory: xtc trr cpt gro g96 pdb tng h5md
  • -s1 [<.tpr>] (top1.tpr) (Optional) — Portable xdr run input file
  • -s2 [<.tpr>] (top2.tpr) (Optional) — Portable xdr run input file
  • -c [<.tpr/.gro/...>] (topol.tpr) (Optional) — Structure+mass(db): tpr gro g96 pdb brk ent
  • -e [<.edr>] (ener.edr) (Optional) — Energy file
  • -e2 [<.edr>] (ener2.edr) (Optional) — Energy file
  • -n [<.ndx>] (index.ndx) (Optional) — Index file

🌼 options to specify output files 🌼

  • -m [<.tex>] (doc.tex) (Optional) — LaTeX file

⭐ other options ⭐

  • -vdwfac <real> (0.8) — Fraction of sum of VdW radii used as warning cutoff
  • -bonlo <real> (0.4) — Min. fract. of sum of VdW radii for bonded atoms
  • -bonhi <real> (0.7) — Max. fract. of sum of VdW radii for bonded atoms
  • -[no]rmsd (no) — Print RMSD for x, v and f
  • -tol <real> (0.001) — Relative tolerance for comparing real values, defined as 2*(a-b)/(|a|+|b|)
  • -abstol <real> (0.001) — Absolute tolerance, useful when sums are close to zero
  • -[no]ab (no) — Compare the A and B topology from one file
  • -lastener <string> — Last energy term to compare (if not given all are tested). It makes sense to go up until the Pressure.

👀 SEE ALSO 👀

the original has a lil line-break hyphen thing in that URL (<‐ at the end of the line) because man pages do that whole hyphenation vibe — the link itself is the gromacs website, ok bestie? 💜

2026, GROMACS development team

and that's the whole page, no notes. this is version 2026.4, dated Oct 02, 2026, from the GROMACS crew — GMX-CHECK(1) and she ate, fr fr. go check ur files, ily, bye 🦋✨💖

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