[gmx-users] Total potential energy: 1/2 protein-solvent interactions??

Xavier Periole X.Periole at rug.nl
Thu Mar 6 12:37:46 CET 2008

> Look at it this way: the total energy is a double sum over all particles. 
>For efficiency one only computes half the matrix, i.e.
> E = sum_{i=1}^N sum_{j=i+1}^N E_{ij}
> however one can also compute it like this:
> E = 1/2 sum_{i=1}^N sum_{j=1}^N E_{ij}
> Now if you define
> E_i = 1/2 sum_{j=1}^N E_{ij}
> then you still have
> E = sum_{i=1}^N E_i
> So that's fine isn't it?
This is fine but it is only technical/algorithmic decomposition, there
is no physical meaning for E_i and associating this to the contribution
of protein and solvent to protein-solvent interaction sounds really
funky !
> I think the interaction energy will level off, even without cutoff (i.e. 
>PME). More later when we've done the work.
Well, the energy should not level off with cutoff that would be totally
counterintuitive, isn't it? If you increase the cutoff the individual
energy contributions decrease but they are many more ... so always a
If it does level off with PME I would become even more allergic to this
method! :))

Can't wait to see the results!


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