GMX-GENCONF(1)

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

✨ GMX-GENCONF(1) — the gmx genconf glow-up ✨

okay bestie, welcome to the GROMACS manual page for gmx-genconf, aka the little tool that multiplies your conformation in "random" orientations 🌸 (yes the quotes are load-bearing, we'll get there). It's giving chaotic good. It's giving wooden blocks. Let's go 💅

🎀 NAME 🎀

gmx-genconf — multiply a conformation in 'random' orientations

🦋 SYNOPSIS 🦋

gmx genconf [-f [<.gro/.g96/...>]] [-trj [<.xtc/.trr/...>]]
            [-o [<.gro/.g96/...>]] [-nbox <vector>] [-dist <vector>]
            [-seed <int>] [-[no]rot] [-maxrot <vector>]
            [-[no]renumber]

💖 DESCRIPTION 💖

so gmx genconf takes a coordinate file and just… multiplies it. It stacks copies on top of each other like a small child playing with wooden blocks 🧱 honestly? iconic behavior.

It builds a grid using proportions you define with -nbox, and then it shoves an extra bit of space between each grid point — that's -dist, bestie.

When the -rot option is switched on, the program does not check for overlap between molecules sitting on grid points. so like, be careful. It is recommended that you make the box in the input file at least as big as the coordinates + the van der Waals radius. no cap, do this 🙈

And if you pass the optional trajectory file, conformations are not generated fresh — they get read from that file and translated appropriately to build the grid. different vibe, same grid 🫶

✨ OPTIONS ✨

🌸 Options to specify input files:

  • -f [<.gro/.g96/...>] (conf.gro) — the structure file. Formats it'll take: gro g96 pdb brk ent esp tpr
  • -trj [<.xtc/.trr/...>] (traj.xtc) (Optional) — the trajectory. Formats: xtc trr cpt gro g96 pdb tng h5md

🦋 Options to specify output files:

  • -o [<.gro/.g96/...>] (out.gro) — the structure file you get out. Formats: gro g96 pdb brk ent esp

💅 Other options:

  • -nbox <vector> (1 1 1) — number of boxes
  • -dist <vector> (0 0 0) — distance between boxes
  • -seed <int> (0) — random generator seed (and 0 means generate, bestie, it doesn't mean "seed of zero")
  • -[no]rot (no) — randomly rotate conformations
  • -maxrot <vector> (180 180 180) — maximum random rotation
  • -[no]renumber (yes) — renumber residues

💀 KNOWN ISSUES 💀

  • The program should allow for random displacement of lattice points.

(yes, that's the whole list. she's a short queen 👑)

⭐ SEE ALSO ⭐

2026, GROMACS development team

and that's the whole page, bestie!! 🫶 this was GROMACS version 2026.4, dated Oct 02, 2026, and honestly? she ate. go multiply something. periodt 💜✨

📦 where this page comes from