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AMBER Archive (2009)Subject: Re: [AMBER] MM-PBSA energy decomposition
From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Hi Dong Xu
> I'd like to know exactly what differences are reflected in the ouptut
Exactly, but assuming you are interested in binding free energies I don't see any conflict here since all internal contributions cancel out in the single trajectory approach and it doesn't matter whether they cancel out in E(INT), E(VDW) or E(ELE).
>
Correct, if you mean nonbonded 1-4 interactions.
>
I don't have an answer here since this is arbitrary in my opinion.
Cheers!
Hannes
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