An optimized replica exchange molecular dynamics method (original) (raw)
Research Article| February 20 2009
Department of Chemistry and Biochemistry, Center for Biological Physics,
Arizona State University
, Tempe, Arizona 85287,
USA
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Department of Chemistry and Biochemistry, Center for Biological Physics,
Arizona State University
, Tempe, Arizona 85287,
USA
Search for other works by this author on:
J. Chem. Phys. 130, 074906 (2009)
We introduce a new way to perform swaps between replicas in replica exchange molecular dynamics simulations. The method is based on a generalized canonical probability distribution function and flattens the potential of mean force along the temperature coordinate, such that a random walk in temperature space is achieved. Application to a Gō model of protein A showed that the method is more efficient than conventional replica exchange. The method results in a constant probability distribution of the replicas over the thermostats, yields a minimum round-trip time between extremum temperatures, and leads to faster ergodic convergence.
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© 2009 American Institute of Physics.
2009
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