AMBER Archive (2009)

Subject: Re: [AMBER] MM-PBSA energy decomposition

From: Hannes Kopitz (Hannes.Kopitz_at_gmx.de)
Date: Thu Apr 30 2009 - 05:37:35 CDT


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

-- 
Neu: GMX FreeDSL Komplettanschluss mit DSL 6.000 Flatrate + Telefonanschluss für nur 17,95 Euro/mtl.!* http://dslspecial.gmx.de/freedsl-surfflat/?ac=OM.AD.PD003K11308T4569a

_______________________________________________ AMBER mailing list AMBER_at_ambermd.org http://lists.ambermd.org/mailman/listinfo/amber