gmx hbond#

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] [-[no]an]
          [-cutoff <real>]

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 hydrogen 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.

-t specifies target selection, relative to which the search for hydrogen 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.

-m forces to merge together information in 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 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 hydrogen bonds in new frame will be stored in its own section of the output index file.

-an forces to accept nitrogen atoms as acceptors of hydrogen bond. If this option is set to ‘false’ state, only oxygen atoms will be considered as acceptors.

-cutoff is a real value that defines distance from donor to acceptor (and vise versa) that used in neighbor search. Minimum (and also recommended) value is 0.35.

-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 hydrogen bonds at the output.

-ang allows you to get a plot of the angular distribution of all hydrogen bonds at the output.

-dan allows you to get a plot of the number of analyzed donors and acceptors 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 writing hydrogen bonds for the whole system.
-[no]an (yes): Accept nitrogen atoms as acceptors of hydrogen bond.
-cutoff <real> (0.35): Distance from donor to acceptor (and vise versa) that used in neighbor search. Must be >= 0.35.