Be aware that these estimators assume no phase transitions. Gaps near a
folding transition may occur.
On Jul 9, 2014 3:49 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Out of curiosity, in your replica log at the very last exchange do you see
> a corresponding dip in exchange acceptance between replicas 55 and 56?
>
> On Wed, Jul 9, 2014 at 12:01 PM, Eugene Yedvabny <eyedvabny.berkeley.edu>
> wrote:
>
> >
> > but for some reason there's almost no exchange between the two groups.
> The
> > behavior suggest there's little overlap between the 55th and 56th
> replica's
> > energy distributions, but I can't rationalize why that would be the case
> > for that particular temperature pair.
> >
>
> Have you looked at the PE overlaps to verify this? It's certainly not out
> the realm of possibility that there is a bug in remlog analysis itself
> (although I really hope not)...
>
> -Dan
>
> PS - Are each of these both from single runs (i.e. one remlog) or from
> multiple runs strung together?
>
>
> >
> > Has anyone seen this kind of behavior in REMD simulations using a ladder
> > from the online calculator? Any suggestions on how to increase the mixing
> > rate and break that barrier would be greatly appreciated! If you also
> have
> > links to other suggested REMD temperate calculators I'd be happy to give
> > them a try.
> >
> > Thank you,
> > Eugene Yedvabny
> >
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> >
> >
>
>
> --
> -------------------------
> Daniel R. Roe, PhD
> Department of Medicinal Chemistry
> University of Utah
> 30 South 2000 East, Room 201
> Salt Lake City, UT 84112-5820
> http://home.chpc.utah.edu/~cheatham/
> (801) 587-9652
> (801) 585-6208 (Fax)
> _______________________________________________
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>
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Received on Wed Jul 09 2014 - 13:30:02 PDT
