Hi
I am using the ff99SB and used the PBradii mbondi2. I am comparing with NMR
experiments.
I am rerunning the simulation with pathches on the termini which seem to
actually reproduce the NMR data better that is why I was wondering if the
desolvation energy from the implicit solvent is too high in my case.
On Mon, Aug 9, 2010 at 1:21 PM, Carlos Simmerling <
carlos.simmerling.gmail.com> wrote:
> 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
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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 - 05:00:04 PDT
