that seems strange- you mean that the GB REMD simulations stay linear? are
you getting good exchange rates, and each replica moves among all
temperatures?
On Mon, Aug 9, 2010 at 11:12 AM, Jorgen Simonsen <jorgen589.gmail.com>wrote:
> hmmm it is actually the opposite - the peptide stays in a linearized form.
> When I run the simulations at 300 K without remd it explores more of the
> compact structures.
> In the explicit simulation the compact is populated with a higher
> probability but this is rarely seen in the REMD simulation.
>
> On Mon, Aug 9, 2010 at 4:20 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > ion pair interactions tend to be too strong in the igb-5/mbondi2
> > combination. check and see if your structures have these present.
> >
> > On Mon, Aug 9, 2010 at 8:02 AM, Jorgen Simonsen <jorgen589.gmail.com>
> > wrote:
> >
> > > Hi
> > >
> > > I use the modified version of GB(igb=5). The NMR experiment was
> performed
> > > at
> > > pH=7 zwitterionic state of the peptides - it does not affect the other
> > > groups in my system but the termini are in their ionic form. The NMR
> data
> > > are averages such as angle and length of different residues H1 coupling
> > > parameters.
> > >
> > > On Mon, Aug 9, 2010 at 1:54 PM, Carlos Simmerling <
> > > carlos.simmerling.gmail.com> wrote:
> > >
> > > > 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
> > > > > > > > > > AMBER.ambermd.org
> > > > > > > > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > >
> > > > > > > > > --
> > > > > > > > > Jason M. Swails
> > > > > > > > > Quantum Theory Project,
> > > > > > > > > University of Florida
> > > > > > > > > Ph.D. Graduate Student
> > > > > > > > > 352-392-4032
> > > > > > > > > _______________________________________________
> > > > > > > > > AMBER mailing list
> > > > > > > > > AMBER.ambermd.org
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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 - 08:30:07 PDT
