I ran a molecular dynamics simulation using Gromacs 2023.2, with the CHARMM36 forcefield. And I ran a per-residue energy decomposition calculation using gmx_MMPBSA, with MMGBSA model. MMGBSA model breaks energy into 1) electrostatic 2) van der waals 3) non-polar solvation 4) polar solvation. By visual inspection of the figure, it seems that electrostatic interactions contributed the most to the protein-ligand complex.

If you use visualization software like Discovery Studio for a protein-ligand complex, it tells you interactions like conventional hydrogen bonding, pi-pi stacking, etc. My question is, is there a clear classification for different interactions in CHARMM36? For example, hydrogen bonding -> van der waals, pi-pi stacking -> van der waals, pi-cation -> electrostatic (just for example, not necessarily correct!). Or maybe I am thinking there is no such clear classification under the hood, instead, CHARMM36 just calculates the energy according to formulas without really caring about what type of interaction it is. As a result, maybe a hydrogen bonding interaction can contribute both electrostatic energy and van der waals.



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