Hydrogen Bond Analysis During Molecular Dynamics

By BioDockify Computational Research Team · August 9, 2026 · MD Analysis

How to analyze hydrogen bonds in MD simulations. Covers H-bond definitions, GROMACS hbond tool, protein-protein and protein-ligand H-bonds, and persistence analysis.

Read the complete article with tables, code and references on BioDockify.

Key References

• Baker, E.N. & Hubbard, R.E. Hydrogen bonding in globular proteins. Prog. Biophys. Mol. Biol. 44, 97-179 (1984).

Scope & Limitations

H-bond definitions vary between tools Geometric criteria are approximate Water-mediated H-bonds require special analysis