Van der Waals interactions

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1

I’m wondering if anyone has any ideas about investigating van der Waals interactions in greater detail. I have calculated the van der Waals energy for a drug-polymer combination and found that it has a greater vdW energy than another drug-polymer combination. Hence, I am curious to investigate what the source of this difference could be. Is there a way in gromacs, or any module, that allows one to investigate this? For example, I know one can use gmx hbond to calculate the number of hydrogen bonds, but I guess hydrogen bonds contribute to electrostatic interactions and not vdW. Thanks!

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2

The decomposition between vdW and Coulombic interaction energy terms is physically meaningless. The total interaction energy may be useful if the force field has been parametrized in such a way that it has basis in physical reality (e.g. CHARMM). Also note that these energies are extrinsic properties; a larger ligand will have a vdW energy with a larger magnitude simply by virtue of having more atoms. That doesn’t tell you anything useful. Of course, this can be normalized against the number of atoms, but again this is not a physically real quantity.