Implementation of a Serial Replica Exchange Method in a Physics-Based United-Residue (UNRES) Force Field.

Abstract

The kinetic-trapping problem in simulating protein folding can be overcome by using a Replica Exchange Method (REM). However, in implementing REM in molecular dynamics simulations, synchronization between processors on parallel computers is required, and communication between processors limits its ability to sample conformational space in a complex system… (More)

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