There have been fairly well-documented shortcomings in the GB model. See
the article
Zhou, R. Free energy landscape of protein folding in water: Explicit vs.
implicit solvent. Proteins 53, 148-161 (2003).
Another thing worth looking into may be the hybrid Explicit/GB REMD done in
the Simmerling group.
Okur, A. et al. Improved Efficiency of Replica Exchange Simulations through
Use of a Hybrid Explicit/Implicit Solvation Model. J Chem Theory Comput 2,
420-433 (2006).
Good luck!
Jason
On Sun, Aug 8, 2010 at 12:44 PM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> Hi,
>
> I am trying to identify the folding of different peptides where the
> sequence
> changes between L-D-L-D etc. I have been running remd for 250 ns in
> implicit
> solvent and 15 ns in explicit solvent and in the case of explicit solvent I
> am able to distinguish and relate to experimental data whereas for the
> implicit solvent the two peptides are more or less identical - has anyone
> experienced similar behavior?
> I know that there should be a difference between implicit and explicit but
> I
> did not expect such a big one though...
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--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Sun Aug 08 2010 - 11:00:05 PDT
