Velocity-scaling optimized replica exchange molecular dynamics of proteins in a hybrid explicit/implicit solvent

Document Type

Article

Publication Date

8-28-2011

Abstract

We propose a scheme for replica exchange molecular dynamics of proteins in explicit solvent that minimizes the number of required replicas using velocity rescaling. Our approach relies on a hybrid method where the protein evolves at each temperature in an explicit solvent, but replica exchange moves utilize an implicit solvent term. The two terms are coupled through the velocity rescaling. We test the efficiency of this approach for a common test case, the trp-cage protein. © 2011 American Institute of Physics.

Publication Title

Journal of Chemical Physics

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