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 efficiently. To minimize communication between processors during the simulation, a Serial Replica Exchange Method (SREM) has been proposed recently by Hagan et al. (J. Phys. Chem. B2007, 111, 1416-1423). Here, we report the implementation of this new SREM algorithm with our physics-based united-residue (UNRES) force field. The method has been tested on the protein 1E0L with a temperature-independent UNRES force field and on terminally blo

SUBMITTER: Shen H 

PROVIDER: S-EPMC2790181 | biostudies-literature | 2008 Aug

REPOSITORIES: biostudies-literature