[AMBER] REMD exchange

From: Francesco Pietra <chiendarret.gmail.com>
Date: Tue, 10 Sep 2013 09:38:25 +0200

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

francesco pietra
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Received on Tue Sep 10 2013 - 01:00:02 PDT
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