Re: [AMBER] MM-PBSA energy decomposition

From: Hannes Kopitz <Hannes.Kopitz.gmx.de>
Date: Thu, 30 Apr 2009 11:37:35 +0100

Hi Dong Xu

> I'd like to know exactly what differences are reflected in the ouptut
> energies using DCTYPE=1/3 vs. 2/4 ?
>
> Do "add 1-4 interactions to bond contributions" refer to E(INT)? But
> E(INT) = 0 with single trajectory approach...

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).

>
> "add 1-4 interactions to either electrostatic or vdW" means 1-4
> interactions are factored into E(ELE) and E(VDW), correct?

Correct, if you mean nonbonded 1-4 interactions.

>
> Would setting DCTYPE=2/4 better than DCTYPE=1/3?

I don't have an answer here since this is arbitrary in my opinion.


Cheers!

Hannes


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Received on Wed May 20 2009 - 13:50:57 PDT
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