Replica-Exchange Accelerated Molecular Dynamics (REXAMD) Applied to Thermodynamic Integration.
Accelerated molecular dynamics (AMD) is an efficient strategy for accelerating the sampling of molecular dynamics simulations, and observable quantities such as free energies derived on the biased AMD potential can be reweighted to yield results consistent with the original, unmodified potential. In conventional AMD the reweighting procedure has an inherent statistical problem in systems with large acceleration, where the points with the largest biases will dominate the reweighted result and reduce the effective number of data points. We propose a replica exchange of various degrees of acceleration (REXAMD) to retain good statistics while achieving enhanced sampling. The REXAMD method is validated and benchmarked on two simple gas-phase model systems, and two different strategies for computing reweighted averages over a simulation are compared.
Fajer
Mikolai
M
Department of Chemistry and Biochemistry, University of California at San Diego, La Jolla, California 92093-0365, Center for Theoretical Biological Physics, University of California at San Diego, La Jolla, California 92039-0365, Department of Chemistry, Georgia State University, Atlanta, Georgia 30302-4098, Department of Pharmacology, University of California at San Diego, La Jolla, California 92093-0365, and Howard Hughes Medical Institute, University of California at San Diego, La Jolla, California 92093-0365.
Hamelberg
Donald
D
McCammon
J Andrew
JA