it will probably help if you tell people what force field you are using,
what solvent model, which set of intrinsic radii, and what experimental data
you are comparing to.
I agree with Dan- be prepared to run hundreds of ns in explicit water, as
the only studies in the literature that include uncertainty estimates are of
this length or longer. much of the early REMD peptide folding literature
with short runs in explicit solvent gives results that we know now are very
likely artifacts of initial conditions. also - my advice is to run twice,
from different initial structures, and only worry about force field when the
2 runs give the same ensembles.
On Mon, Aug 9, 2010 at 3:02 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> 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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> >
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Received on Mon Aug 09 2010 - 04:30:03 PDT
