Yes I am also puzzled about the results. In the GB I didn't not have any
patches on the peptides(in the explicit the same no patches) but I was
wondering if the desolvation energy could be to high? So I am running some
modifications and elongating my explicit solvation simulation.
On Mon, Aug 9, 2010 at 8:54 AM, Daniel Sindhikara <sindhikara.gmail.com>wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> 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 - 00:30:03 PDT
