[gmx-users] System equilibration and interaction energy
Mark.Abraham at anu.edu.au
Fri Apr 28 05:45:05 CEST 2006
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.
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