title: An optimized replica exchange molecular dynamics method.
abstract: 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 Go 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.
authors.affiliation: Department of Chemistry and Biochemistry, Center for Biological Physics, Arizona State University, Tempe, Arizona 85287, USA.
authors.forename: Hiqmet
authors.initials: H
authors.lastname: Kamberaj
authors.forename: Arjan
authors.initials: A
authors.lastname: van der Vaart
mesh_terms: D000465:Algorithms; D006358:Hot Temperature; D008958:Models, Molecular; D011336:Probability; D011489:Protein Denaturation; D017510:Protein Folding; D017433:Protein Structure, Secondary; D013205:Staphylococcal Protein A / Q000737:chemistry; D013816:Thermodynamics
chemical_list: D013205:Staphylococcal Protein A