Andrzej Kolinski Research Group

Coarse-grained protein modeling

Modeling Software & Servers

Biomolecules — dynamics & interactions

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Velocity scaling for optimizing replica exchange molecular dynamics

Source:

The Journal of Chemical Physics, AIP, 134:044124, 2011

Abstract

We discuss the use of velocity rescaling for generating rejection-free exchange moves in replica exchange molecular dynamics. We test the efficiency of this approach for a common test case, the trp-cage protein. Advantages and limitations of the approach are discussed and possible extensions outlined.