title: Distributed Replica Sampling.
abstract: We present a simple and general scheme for efficient Boltzmann sampling of conformational space by computer simulation. Multiple replicas of the system differing in temperature T or reaction coordinate λ are simulated independently. In addition, occasional stochastic moves of individual replicas in T or λ space are considered one at a time on the basis of a generalized Hamiltonian containing an extra potential energy term or bias that depends on the distribution of all replicas. The algorithm is inherently suited for shared or heterogeneous computing platforms such as a distributed network.
authors.affiliation: Structural Biology and Biochemistry, The Hospital for Sick Children, 555 University Ave., Toronto, Ontario, Canada M5G 1X8, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 4 Taddle Creek Road, Rm. 407, Rosebrugh Building, Toronto, Ontario, Canada M5S 3G9.
authors.forename: Tomas
authors.initials: T
authors.lastname: Rodinger
authors.affiliation: Structural Biology and Biochemistry, The Hospital for Sick Children, 555 University Ave., Toronto, Ontario, Canada M5G 1X8, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 4 Taddle Creek Road, Rm. 407, Rosebrugh Building, Toronto, Ontario, Canada M5S 3G9.
authors.forename: P Lynne
authors.initials: PL
authors.lastname: Howell
authors.affiliation: Structural Biology and Biochemistry, The Hospital for Sick Children, 555 University Ave., Toronto, Ontario, Canada M5G 1X8, Department of Biochemistry, University of Toronto, 1 King's College Circle, Toronto, Ontario, Canada M5S 1A8, and Institute of Biomaterials and Biomedical Engineering, University of Toronto, 4 Taddle Creek Road, Rm. 407, Rosebrugh Building, Toronto, Ontario, Canada M5S 3G9.
authors.forename: Régis
authors.initials: R
authors.lastname: Pomès