you don't say which GB, or what kind of NMR data. what was the pH of the NMR
experiment? Does it affect your protonation states? What are the termini in
the NMR?
On Mon, Aug 9, 2010 at 7:52 AM, Jorgen Simonsen <jorgen589.gmail.com> wrote:
> 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...
> > > > > > _______________________________________________
> > > > > > AMBER mailing list
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> > > > > >
> > > > >
> > > > >
> > > > >
> > > > > --
> > > > > Jason M. Swails
> > > > > Quantum Theory Project,
> > > > > University of Florida
> > > > > Ph.D. Graduate Student
> > > > > 352-392-4032
> > > > > _______________________________________________
> > > > > AMBER mailing list
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> > > > > 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 - 05:00:05 PDT
