[gmx-users] System equilibration and interaction energy

[Mark Abraham]

aloks at mbu.iisc.ernet.in wrote:
> Thanks a lot Mark for your prompt reply. but i have another doubt, if we
> sum all the pair wise energies (lj and coul.) in that case we will miss
> water mediated protein ligand interactions, which i am expecting to be
> present in my case, based on crstyal structure. what would be the best way
> to consider those interactions also in account?

I think you're trying to achieve an impossible level of additivity. 
There will be a continuum of significance for all of the solvent 
molecules in the system... where can you draw a line?

Fundamentally the whole interaction is concerted... there's a fair case 
for being skeptical about the meaning of an interaction energy such as I 
described even when there is no direct solvent mediation.

Mark