GMX-DISTANCE(1)

💖 GMX-DISTANCE(1) — gmx-distance 💖

okay bestie, so this is a page from the GROMACS manual set, section 1. it's gmx-distance, and it's literally about measuring how far apart things are. strap in. 🎀

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✨ NAME ✨

gmx-distance — calculate distances between pairs of positions 📏

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🌸 SYNOPSIS 🌸

gmx distance [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
             [-oav [<.xvg>]] [-oall [<.xvg>]] [-oxyz [<.xvg>]]
             [-oh [<.xvg>]] [-oallstat [<.xvg>]] [-b <time>]
             [-e <time>] [-dt <time>] [-tu <enum>]
             [-fgroup <selection>] [-xvg <enum>] [-[no]rmpbc]
             [-[no]pbc] [-sf <file>] [-selrpos <enum>]
             [-seltype <enum>] [-select <selection>] [-len <real>]
             [-tol <real>] [-binw <real>]

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🦋 DESCRIPTION 🦋

so gmx distance calculates distances between pairs of positions as a function of time. like, it's giving timeline energy. ⏳

each selection specifies an independent set of distances to calculate. each selection should consist of pairs of positions, and the distances are computed between positions 1-2, 3-4, etc. no cap.

-oav writes the average distance as a function of time for each selection. -oall writes all the individual distances. -oxyz does the same, but the x, y, and z components of the distance are written instead of the norm. -oh writes a histogram of the distances for each selection. the location of the histogram is set with -len and -tol. bin width is set with -binw. -oallstat writes out the average and standard deviation for each individual distance, calculated over the frames. 📊

⚠️ note that gmx distance calculates distances between fixed pairs (1-2, 3-4, etc.) within a single selection. if you wanna calculate distances between two selections — including minimum, maximum, and pairwise distances — use gmx pairdist instead. don't be out here using the wrong tool bestie 😭

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💅 OPTIONS 💅

🫶 options to specify input files

• -f [<.xtc/.trr/...>] (traj.xtc) (Optional) — input trajectory or single configuration, and the formats it'll take are: 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

• -oav [<.xvg>] (distave.xvg) (Optional) — average distances as function of time
• -oall [<.xvg>] (dist.xvg) (Optional) — all distances as function of time
• -oxyz [<.xvg>] (distxyz.xvg) (Optional) — distance components as function of time
• -oh [<.xvg>] (disthist.xvg) (Optional) — histogram of the distances
• -oallstat [<.xvg>] (diststat.xvg) (Optional) — statistics for individual distances

✨ 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
• -select <selection> — position pairs to calculate distances for
• -len <real> (0.1) — mean distance for histogramming
• -tol <real> (1) — width of full distribution as fraction of -len
• -binw <real> (0.001) — bin width for histogramming

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👑 SEE ALSO 👑

• gmx(1)

more info about GROMACS is available at <http://www.gromacs.org/>. 🌈

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💜 COPYRIGHT 💜

2026, GROMACS development team

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and that's the whole page bestie, you ate that 💅✨ ok so final sign-off: this was 2026.4, dated Oct 02, 2026, and the page itself is GMX-DISTANCE(1) from the GROMACS fam. go measure some distances, you main character 🦋💖