Jason is right about the shortcomings of GB. But you are comparing 200 ns
REMD GB
vs 15 ns explicit? My assumption is that if you need 200 ns to converge in
GB you need
longer than that to converge explicit. Your results may just be an artifact
of the initial structure.
So it may not be a problem with GB solvent, but one of the force field.
Regardless I wouldn't
make and conclusions until I was convinced the simulations were reasonable
converged.
--Dan
On Mon, Aug 9, 2010 at 2:47 AM, Jason Swails <jason.swails.gmail.com> wrote:
> 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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>
--
Dr. Daniel J. Sindhikara
Institute for Molecular Science
E-mail: sindhikara.gmail.com
Website: http://sites.google.com/site/dansindhikara/
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Received on Mon Aug 09 2010 - 00:00:06 PDT
