GMX-HBOND(1)

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version 2026.4 · 8 versions
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💅 GMX-HBOND(1) — the gmx-hbond page, bestie edition 💖

okay so real talk: this is the manual page for gmx-hbond, part of the GROMACS suite, sitting in manual section 1. It computes and analyzes hydrogen bonds, and it's lowkey iconic. Let's go 🦋

✨ NAME ✨

gmx-hbond — compute and analyze hydrogen bonds 🌸

✨ SYNOPSIS ✨

gmx hbond [-f [<.xtc/.trr/...>]] [-s [<.tpr/.gro/...>]] [-n [<.ndx>]]
          [-o [<.ndx>]] [-num [<.xvg>]] [-dist [<.xvg>]]
          [-ang [<.xvg>]] [-dan [<.xvg>]] [-b <time>] [-e <time>]
          [-dt <time>] [-tu <enum>] [-fgroup <selection>]
          [-xvg <enum>] [-[no]rmpbc] [-[no]pbc] [-sf <file>]
          [-selrpos <enum>] [-seltype <enum>] [-r <selection>]
          [-t <selection>] [-[no]m] [-[no]pf] [-cutoff <real>]
          [-hbr <real>] [-hba <real>] [-de <string>] [-ae <string>]

✨ DESCRIPTION ✨

gmx hbond lets you use a geometric definition of hydrogen bonds to define them throughout the whole structure. Basically: vibe check every possible H-bond, no cap. 💅

  • -r specifies the reference selection, relative to which the search for hydrogen bonds in the target selection will develop. Not me warning you though: note that all atoms in reference and target selections should be either absolutely identical or non-overlapping at all. Accepts dynamic selection. 🫶
  • -t specifies the target selection, relative to which the search for hydrogen bonds in the reference selection will develop. Same energy as -r: all atoms in reference and target selections should be either absolutely identical or non-overlapping at all. Accepts dynamic selection. ✨
  • -m forces you to merge together information in the output index file about hydrogen bonds if they differ only in hydrogen indices. This also means that information about hydrogen atoms in the hydrogen bonds would not be written in the output index file at all. 🙈
  • -pf forces writing hydrogen bonds for each frame separately instead of writing hydrogen bonds for the whole system. Each bit of information about hydrogen bonds in a new frame will be stored in its own section of the output index file. 📚
  • -cutoff is a real value that defines the distance from donor to acceptor (and vice versa) that's used in the neighbor search. The minimum (and also recommended) value is 0.35. 💀
  • -hbr sets the cutoff used when calculating hydrogen bond distances. Recommended value: 0.35. 🔥
  • -hba sets the cutoff used when calculating hydrogen bond angles. Recommended value: 30. 📐
  • -de specifies the atomic elements that will be selected from the topology to check if a given element is a potential hydrogen bond donor. 👑
  • -ae specifies the atomic elements that will be selected from the topology to check if a given element is a potential hydrogen bond acceptor. 🎀
  • -num lets you get a plot of the number of hydrogen bonds as a function of time at the output. 📈
  • -dist lets you get a plot of the distance distribution of all hydrogen bonds at the output. 🌈
  • -ang lets you get a plot of the angular distribution of all hydrogen bonds at the output. ⭐
  • -dan lets you get a plot of the number of analyzed donors and acceptors for each frame at the output. 🍓
Heads up bestie: note that this is a new implementation of the hbond utility added in GROMACS 2024. If you need the old one, use gmx hbond-legacy. Choose wisely, both are valid. 💖

✨ OPTIONS ✨

🌸 Options to specify input files:

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

🌸 Options to specify output files:

  • -o [<.ndx>] (default hbond.ndx) — Index file that contains selected groups', acceptors', donors' and hydrogens' indices and hydrogen bond pairs between or within selected groups. 💅
  • -num [<.xvg>] (default hbnum.xvg) (Optional) — Number of hydrogen bonds as a function of time. 📈
  • -dist [<.xvg>] (default hbdist.xvg) (Optional) — Distance distribution of all hydrogen bonds. 🌸
  • -ang [<.xvg>] (default hbang.xvg) (Optional) — Angle distribution of all hydrogen bonds. 📐
  • -dan [<.xvg>] (default hbdan.xvg) (Optional) — Number of donors and acceptors analyzed for each frame. 🍓

🌸 Other options:

  • -b <time> (default 0) — First frame (ps) to read from trajectory ⏰
  • -e <time> (default 0) — Last frame (ps) to read from trajectory ⏰
  • -dt <time> (default 0) — Only use frame if t MOD dt == first time (ps) 🕰️
  • -tu <enum> (default 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> (default xmgrace) — Plot formatting: xmgrace, xmgr, none 🎨
  • -[no]rmpbc (default yes) — Make molecules whole for each frame 🧩
  • -[no]pbc (default yes) — Use periodic boundary conditions for distance calculation 🔁
  • -sf <file> — Provide selections from files 📁
  • -selrpos <enum> (default 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> (default 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 🎯
  • -r <selection> — Reference selection, relative to which the search for hydrogen bonds in target selection will develop. 🦋
  • -t <selection> — Target selection, relative to which the search for hydrogen bonds in reference selection will develop. 🦋
  • -[no]m (default no) — Merge together information about hydrogen bonds if they differ only in hydrogen indices. 🙈
  • -[no]pf (default no) — Write hydrogen bonds for each frame separately instead of writing hydrogen bonds for the whole system. 📚
  • -cutoff <real> (default 0.35) — Distance from donor to acceptor (and vice versa) that used in neighbor search (nm). Must be > 0. ⚠️
  • -hbr <real> (default 0.35) — Hydrogen bond cutoff distance, between donor and acceptor (nm). The value must not exceed the neighbor search cutoff and must be > 0. ⚠️
  • -hba <real> (default 30) — A-D-H hydrogen bond cutoff angle (degrees). Must be > 0. ⚠️
  • -de <string> (default N O) — Donor elements. Default elements: N, O. 👑
  • -ae <string> (default N O) — Acceptor elements. Default elements: N, O. 🎀

✨ SEE ALSO ✨

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

2026, GROMACS development team — periodt. 💜

and that's the whole page, bestie!! this was GROMACS 2026.4, dated Oct 02, 2026, brought to you by the GROMACS development team — mwah, go analyze some hydrogen bonds, you main character 🫶✨💖

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