GMX-PAIRDIST(1)

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

💖 GMX-PAIRDIST(1) 💖

okay bestie, welcome to GROMACS section 1 — this is gmx-pairdist, and no cap, it's the little tool that ✨ measures how far apart your stuff is ✨

💅 NAME 💅

gmx-pairdist — calculate pairwise distances between groups of positions. that's it, that's the whole job, and it does it gorgeously 🫶

🎀 SYNOPSIS 🎀

gmx pairdist [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
             [-o [<.xvg>]] [-b <time>] [-e <time>] [-dt <time>]
             [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
             [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
             [-seltype <enum>] [-cutoff <real>] [-type <enum>]
             [-refgrouping <enum>] [-selgrouping <enum>]
             [-ref <selection>] [-sel <selection>]

like yes she has a lot of flags, but she's worth it 💖

✨ DESCRIPTION ✨

so gmx pairdist computes pairwise distances between one reference selection (you give her that with -ref) and one or more other selections (those go in -sel). iconic behavior tbh.

she can calculate either the minimum distance (that's the default, she's a lowballer bestie 💀) or the maximum distance (that's with -type max). and the distances to each selection you hand over with -sel are computed independently — no crossover drama, they mind their own business 🧚

by default she computes the global minimum/maximum distance. but bestie, if you want more distances — like, say, minimum distances to each residue in -ref — then you use -refgrouping and/or -selgrouping to specify how the positions within each selection should be grouped. that's the whole trick 🎀

computed distances get written to the file you specify with -o. now here's the math, and I need you to lock in: if there are N groups in -ref and M groups in the first selection in -sel, then the output contains N*M columns for the first selection. the columns contain distances like this: r1-s1, r2-s1, ..., r1-s2, r2-s2, ..., where rn is the n'th group in -ref and sn is the n'th group in the other selection. and the distances for the second selection come as separate columns after the first selection, and so on. periodt. 💅

if some selections are dynamic, only the selected positions are used in the computation — but the same number of columns is always written out. the column count does not care about your feelings, she is consistent 👑

and if there are no positions contributing to some group pair? then the cutoff value is written instead (see below). imagine being that group pair. couldn't be me 😭

-cutoff sets a cutoff for the computed distances. if the result would contain a distance over the cutoff, the cutoff value is written to the output file instead. by default, no cutoff is used — but!! if you're not interested in values beyond a cutoff, or if you know that the minimum distance is smaller than a cutoff, you should set this option, because it lets the tool use grid-based searching and be significantly faster. glow up via one flag, we love to see it 🔥

ngl, if you want to compute distances between fixed pairs, gmx distance may be a more suitable tool. just saying, don't make pairdist do a job that isn't hers 🫶

🌸 OPTIONS 🌸

💜 Options to specify input files:

  • -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — input trajectory or single configuration. formats she eats: xtc trr cpt gro g96 pdb tng h5md
  • -s [<.tpr/.gro/...>] (topol.tpr) (Optional) — input structure. formats: tpr gro g96 pdb brk ent
  • -n [<.ndx>] (index.ndx) (Optional) — extra index groups

💖 Options to specify output files:

  • -o [<.xvg>] (dist.xvg) — distances as function of time 📈

🦋 Other options:

  • -b <time> (0) — first frame (ps) to read from trajectory
  • -e <time> (0) — last frame (ps) to read from trajectory
  • -dt <time> (0) — only use frame if t MOD dt == first time (ps)
  • -tu <enum> (ps) — unit for time values: fs, ps, ns, us, ms, s
  • -fgroup <selection> — atoms stored in the trajectory file (if not set, assume first N atoms)
  • -xvg <enum> (xmgrace) — plot formatting: xmgrace, xmgr, none
  • -[no]rmpbc (yes) — make molecules whole for each frame
  • -[no]pbc (yes) — use periodic boundary conditions for distance calculation
  • -sf <file> — provide selections from files
  • -selrpos <enum> (atom) — selection reference positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
  • -seltype <enum> (atom) — default selection output positions: atom, res_com, res_cog, mol_com, mol_cog, whole_res_com, whole_res_cog, whole_mol_com, whole_mol_cog, part_res_com, part_res_cog, part_mol_com, part_mol_cog, dyn_res_com, dyn_res_cog, dyn_mol_com, dyn_mol_cog
  • -cutoff <real> (0) — maximum distance to consider
  • -type <enum> (min) — type of distances to calculate: min, max
  • -refgrouping <enum> (all) — grouping of -ref positions to compute the min/max over: all, res, mol, none
  • -selgrouping <enum> (all) — grouping of -sel positions to compute the min/max over: all, res, mol, none
  • -ref <selection> — reference positions to calculate distances from
  • -sel <selection> — positions to calculate distances for

👑 SEE ALSO 👑

more info about GROMACS is available at <http://www.gromacs.org/>. bestie, go read it, it's giving knowledge 🌈

2026, GROMACS development team

that's the whole page, you ate it, I'm so proud of you 💖✨

this was GROMACS 2026.4, dated Oct 02, 2026, brought to you by the GROMACS development team — mwah, kisses, go measure some distances 🎀💅🫶

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