GMX-MINDIST(1)

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

✨ gmx-mindist ✨

okay bestie, welcome to gmx-mindist from the GROMACS fam (section 1, if you're keeping track) 💖 she's the one you call when you need to know how close two groups of atoms are getting. respectfully. 👀

🎀 NAME 🎀

gmx-mindist — calculate the minimum distance between two groups

Like literally. That's her whole job. And she ate. 💅

🦋 SYNOPSIS 🦋

gmx mindist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
            [-od [<.xvg>]] [-on [<.xvg>]] [-o [<.out>]]
            [-ox [<.xtc/.trr/...>]] [-or [<.xvg>]] [-b <time>]
            [-e <time>] [-dt <time>] [-tu <enum>] [-[no]w]
            [-xvg <enum>] [-[no]matrix] [-[no]max] [-d <real>]
            [-[no]group] [-[no]pi] [-[no]split] [-ng <int>]
            [-[no]pbc] [-[no]respertime] [-[no]printresname]

🌸 DESCRIPTION 🌸

so gmx mindist computes the distance between one group and a number of other groups. she's social like that. 🫶

and she gives you two things (into two separate output files, because she's organized):

  • the minimum distance between any pair of atoms from the respective groups
  • the number of contacts within a given distance

lowkey iconic. two for one. 💅

With the -group option, a contact of an atom in another group with multiple atoms in the first group gets counted as one contact instead of as multiple contacts. so no double-dipping, we count it once, periodt. ✋

With -or, minimum distances to each residue in the first group are determined and plotted as a function of residue number. per-residue breakdown, we love to see it. 💖

With option -pi the minimum distance of a group to its periodic image is plotted. this is useful for checking if a protein has seen its periodic image during a simulation (yes bestie, proteins get glances too). Only one shift in each direction is considered, giving a total of 26 shifts. ⭐

note that periodicity information is required from the file supplied with -s, either as a .tpr file or a .pdb file with CRYST1 fields. no periodicity info = no vibe. 🚫

it also plots the maximum distance within the group and the lengths of the three box vectors. she's thorough. she's giving main character energy. 👑

Also gmx distance and gmx pairdist calculate distances. just so you know your options, iykyk. 🌈

💜 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) (Optional) — Structure+mass(db): tpr gro g96 pdb brk ent
  • -n [<.ndx>] (index.ndx) (Optional) — Index file

🧚 Options to specify output files:

  • -od [<.xvg>] (mindist.xvg) — xvgr/xmgr file
  • -on [<.xvg>] (numcont.xvg) (Optional) — xvgr/xmgr file
  • -o [<.out>] (atm-pair.out) (Optional) — Generic output file
  • -ox [<.xtc/.trr/...>] (mindist.xtc) (Optional) — Trajectory: xtc trr gro g96 pdb tng h5md
  • -or [<.xvg>] (mindistres.xvg) (Optional) — xvgr/xmgr 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)
  • -tu <enum> (ps) — Unit for time values: fs, ps, ns, us, ms, s
  • -[no]w (no) — View output .xvg, .xpm, .eps and .pdb files
  • -xvg <enum> (xmgrace) — xvg plot formatting: xmgrace, xmgr, none
  • -[no]matrix (no) — Calculate half a matrix of group-group distances
  • -[no]max (no) — Calculate maximum distance instead of minimum
  • -d <real> (0.6) — Distance for contacts
  • -[no]group (no) — Count contacts with multiple atoms in the first group as one
  • -[no]pi (no) — Calculate minimum distance with periodic images
  • -[no]split (no) — Split graph where time is zero
  • -ng <int> (1) — Number of secondary groups to compute distance to a central group
  • -[no]pbc (yes) — Take periodic boundary conditions into account
  • -[no]respertime (no) — When writing per-residue distances, write distance for each time point
  • -[no]printresname (no) — Write residue names

🔥 SEE ALSO 🔥

More information about GROMACS is available at <http://www.gromacs.org/>. 🦋

2026, GROMACS development team

okay that's the whole thing bestie, no cap, you're now officially fluent in gmx-mindist 💖 this was version 2026.4, dated Oct 02, 2026 — go forth and measure some distances, you absolute icon 🎀✨💅

📦 where this page comes from