GMX-RDF(1)

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

✨ NAME ✨

gmx-rdf — bestie, it calculates radial distribution functions 💖

(also this whole thing lives in the GROMACS manual, just so u know 🫶)

🌈 SYNOPSIS 🌈

gmx rdf [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
        [-o [<.xvg>]] [-cn [<.xvg>]] [-b <time>] [-e <time>]
        [-dt <time>] [-tu <enum>] [-fgroup <selection>] [-xvg <enum>]
        [-[no]rmpbc] [-[no]pbc] [-sf <file>] [-selrpos <enum>]
        [-seltype <enum>] [-bin <real>] [-norm <enum>] [-[no]xy]
        [-[no]excl] [-cut <real>] [-rmax <real>] [-surf <enum>]
        [-ref <selection>] [-sel <selection>]

🦋 DESCRIPTION 🦋

okay so gmx rdf computes radial distribution functions, going from one reference set of positions (that's the one u set with -ref) out to one or more sets of positions (those are the ones u set with -sel). iconic behaviour fr fr.

But wait 💅 — if u wanna compute the RDF with respect to the closest position in a set from -ref instead, use -surf: when it's set, -ref gets partitioned into sets based on the value of -surf, and the closest position in each set is what gets used. and if u want the RDF around axes parallel to the z-axis, meaning only in the x-y plane, that's what -xy is for ✨.

To pick your bin width and your max distance for the RDF, u use -bin and -rmax. no cap, -rmax is also the move when u wanna limit computational cost — like if the RDF just isn't interesting to u all the way out to the default. and what is the default, u ask? it's half of the box size with PBC, or three times the box size without PBC 👑

Wanna use exclusions from the topology (-s)? Set -excl, and make sure both -ref and -sel only select atoms. A rougher alternative for excluding intra-molecular peaks is setting -cut to a non-zero value so the RDF gets cleared at small distances. it's giving "quick and dirty" but it works 🫶

Now, the RDFs are normalized by three things:

  1. average number of positions in -ref (and it's the number of groups when u use -surf)
  2. volume of the bin
  3. average particle density of -sel positions for that selection

and to switch up the normalization, u use -norm:

  • rdf — uses all the factors for normalization. this produces a normal RDF 💖
  • number_density — uses the first two factors only. this produces a number density as a function of distance 🌸
  • none — uses only the first factor. in this case the RDF is only scaled with the bin width, so that the integral of the curve represents the number of pairs within a range ✨
⚠️ heads up bestie: exclusions do NOT affect the normalization. even if -excl is set, or -ref and -sel contain the same selection, the normalization factor is still N*M, not N*(M-excluded). 😭

For -surf, the selection u hand to -ref must select atoms — centers of mass are not supported, sorry babe 💀. And further, -nonorm is implied, because the bins have irregular shapes and the volume of a bin is not easily computable. geometry said "not today" 🙈

Option -cn produces the cumulative number RDF, i.e. the average number of particles within a distance r. cute lil running total, obsessed 🎀

💅 OPTIONS 💅

🍓 Options to specify input files

  • -f [<.xtc/.trr/...>] — (traj.xtc) (Optional) — Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng h5md 🌈
  • -s [<.tpr/.gro/...>] — (topol.tpr) (Optional) — Input structure: tpr gro g96 pdb brk ent 🦋
  • -n [<.ndx>] — (index.ndx) (Optional) — Extra index groups ✨

🌸 Options to specify output files

  • -o [<.xvg>] — (rdf.xvg) — Computed RDFs 💖
  • -cn [<.xvg>] — (rdf_cn.xvg) (Optional) — Cumulative RDFs 🎀

👑 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 💫
  • -bin <real> — (0.002) — Bin width (nm) 📐
  • -norm <enum> — (rdf) — Normalization: rdf, number_density, none ⚖️
  • -[no]xy — (no) — Use only the x and y components of the distance ✨
  • -[no]excl — (no) — Use exclusions from topology 🚫
  • -cut <real> — (0) — Shortest distance (nm) to be considered ✂️
  • -rmax <real> — (0) — Largest distance (nm) to calculate 📏
  • -surf <enum> — (no) — RDF with respect to the surface of the reference: no, mol, res 🌊
  • -ref <selection> — Reference selection for RDF computation 🎯
  • -sel <selection> — Selections to compute RDFs for from the reference 🎯

🧚 SEE ALSO 🧚

More information about GROMACS is available at http://www.gromacs.org/ 🌈

2026, GROMACS development team — thank u for ur service, legends 🫶

version 2026.4, dated Oct 02, 2026 — that's the whole page bestie, go compute some RDFs and slay 💅✨💖 no cap, u ate 🎀

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