On Tue, Sep 10, 2013 at 3:38 AM, Francesco Pietra <chiendarret.gmail.com>wrote:
> Hello:
> I am progressing toward a major task of carrying out a pure T-remd
> (parallel tempering) with a 34aa peptide in explicit water for a 314-600K
> range. After C. Simmerling reports about implic media, I did not attempt
> any simulation under implicit media.
>
> I started with 8 replicas and geom progressing temp, noticing, for the
> 314-320K range, full exchange is obtained. deltaT is 0.8K.
>
> On increasing the nr of replicas and delta T on the above basis, thus 16
> replicas for 314-326K, the exchange is no more so good. That is, the
> highest and the lowest temp do not exchange with one another directly.
>
> My question is, do, for example, exchange of 16 with 15 only, and exchange
> of 14 with 15, compensate? In other words, do "local exchanges" propagate?
>
> In this affair, I restrained the dihedrals for a two (starting) alpha
> helical turns, which are well defined by X-ray diffraction. The rest of the
> peptide does not clearly diffract at 100K, and I am attempting to simulate
> how the conformation, or prevailing cluster of conformations, should be. I
> did not apply any other restraint to this undefined part. Should the
> chirality at the peptide bond be imposed even if the prevailing
> conformation is unknown?
>
> Thanks so much for advice
>
Assuming that I am interpreting your question correctly, there is no need
to achieve exchanges between the first and last temperature replica. In
fact, if you are achieving exchanges between those two a high percentage of
the time, then all of the replicas in between are unnecessary :). As long
as adjacent replicas exchange frequently enough (about 20% of the time is
good in my experience), then you will get good enough mixing in state space
to make efficient use of REMD. (Replicas will be able to diffuse through
state space from the lowest temperature to the highest _through_ the
intermediate temperatures).
The following website will give you a good set of starting temperatures
between two replicas: http://folding.bmc.uu.se/remd/ (the NPT results are
good enough for the NVT REMD that Amber runs). It may be worth running a
quick simulation to verify that all exchange rates are approximately what
you want them to be before starting major production.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Sep 10 2013 - 04:30:03 PDT
