On Apr 9, 2012, at 7:16 PM, Aron Broom <broomsday.gmail.com> wrote:
> Carlos,
>
> I'm slightly confused, does this mean that without the SASA term it would
> actually be *harder* to expose a hydrophobic region to solvent because
> there is no compensatory VDW term?
I don't think he's saying that. The lack of compensatory VDW is, in my view, a fortuitous cancellation of errors (but perhaps there is some more physical meaning to it that I'm not aware of).
I imagine that GB does not benefit from some of the intrinsic properties of explicit solvent (specifically relating to solvent orientation and organization --entropic effects of the water, perhaps) that deter hydrophobic exposure, but the lack of compensatory VDW interactions fortuitously has the same effect for GB. I would also guess that because VDW interactions are so weak, this is sometimes not enough, so the SASA term is there to help out when necessary.
Given that the energy varies linearly with the SASA, this term should always aim to minimize the exposed surface area. However, I don't have a very good feel for the physical significance of the LCPO gradients and how they actually relate to whatever the "true" non-polar gradients are (whatever those should be), so while I expect the behavior I described should be true, it's not obvious to me that the LCPO forces necessarily imply that (but I am no expert on LCPO).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Apr 09 2012 - 21:30:03 PDT
