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GMX-HBOND(1) GROMACS GMX-HBOND(1) 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 allows using geometric definition of hydrogen bonds to define them throughout the structure. -r specifies reference selection, relative to which the search for hy- drogen bonds in target selection will develop. Note that all atoms in reference and target selections should be either absolutely identical or non-overlapping at all. Accepts dynamic selection. -t specifies target selection, relative to which the search for hydro- gen bonds in reference selection will develop. Note that all atoms in reference and target selections should be either absolutely identical or non-overlapping at all. Accepts dynamic selection. -m forces to merge together information in output index file about hy- drogen 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 output index file at all. -pf forces to write hydrogen bonds for each frame separately instead of writing hydrogen bonds for the whole system. Each information about hy- drogen bonds in new frame will be stored in its own section of the out- put index file. -cutoff is a real value that defines distance from donor to acceptor (and vice versa) that used in neighbor search. Minimum (and also recom- mended) value is 0.35. -hbr Sets the cutoff that is used when calculating hydrogen bond dis- tances. Recommended value: 0.35. -hba Sets the cutoff that is used when calculating hydrogen bond an- gles. Recommended value: 30. -de Specifies the atomic elements that will be selected from the topol- ogy to check if a given element is a potential hydrogen bond donor. -ae Specifies the atomic elements that will be selected from the topol- ogy to check if a given element is a potential hydrogen bond acceptor. -num allows you to get a plot of the number of hydrogen bonds as a function of time at the output. -dist allows you to get a plot of the distance distribution of all hy- drogen bonds at the output. -ang allows you to get a plot of the angular distribution of all hydro- gen bonds at the output. -dan allows you to get a plot of the number of analyzed donors and ac- ceptors for each frame at the output. 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. OPTIONS Options to specify input files: -f [<.xtc/.trr/...>] (traj.xtc) (Optional) Input trajectory or single configuration: xtc trr cpt gro g96 pdb tng -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 [<.ndx>] (hbond.ndx) Index file that contains selected groups', acceptors', donors' and hydrogens' indices and hydrogen bond pairs between or within selected groups. -num [<.xvg>] (hbnum.xvg) (Optional) Number of hydrogen bonds as a function of time. -dist [<.xvg>] (hbdist.xvg) (Optional) Distance distribution of all hydrogen bonds. -ang [<.xvg>] (hbang.xvg) (Optional) Angle distribution of all hydrogen bonds. -dan [<.xvg>] (hbdan.xvg) (Optional) Number of donors and acceptors analyzed for each frame. 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 -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 (no) Merge together information about hydrogen bonds if they differ only in hydrogen indices. -[no]pf (no) Write hydrogen bonds for each frame separately instead of writ- ing hydrogen bonds for the whole system. -cutoff <real> (0.35) Distance from donor to acceptor (and vice versa) that used in neighbor search (nm). Must be > 0. -hbr <real> (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> (30) A-D-H hydrogen bond cutoff angle (degrees). Must be > 0. -de <string> (N O) Donor elements. Default elements: N, O. -ae <string> (N O) Acceptor elements. Default elements: N, O. SEE ALSO gmx(1) More information about GROMACS is available at <- http://www.gromacs.org/>. COPYRIGHT 2025, GROMACS development team 2025.0 Feb 10, 2025 GMX-HBOND(1)
NAME | SYNOPSIS | DESCRIPTION | OPTIONS | SEE ALSO | COPYRIGHT
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