title: Resolution Exchange Simulation with Incremental Coarsening.
abstract: We previously developed an algorithm, called "resolution exchange", which improves canonical sampling of atomic resolution models by swapping conformations between high- and low-resolution simulations. Here, we demonstrate a generally applicable incremental coarsening procedure and apply the algorithm to a larger peptide, met-enkephalin. In addition, we demonstrate a combination of resolution and temperature exchange, in which the coarser simulations are also at elevated temperatures. Both simulations are implemented in a "top-down" mode, to allow efficient allocation of CPU time among the different replicas.
authors.affiliation: Department of Computational Biology, School of Medicine, and Department of Environmental and Occupational Health, Graduate School of Public Health, BST W1041, 200 Lothrop Street, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.
authors.forename: Edward
authors.initials: E
authors.lastname: Lyman
authors.affiliation: Department of Computational Biology, School of Medicine, and Department of Environmental and Occupational Health, Graduate School of Public Health, BST W1041, 200 Lothrop Street, University of Pittsburgh, Pittsburgh, Pennsylvania 15261.
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Zuckerman