title: Simulated-tempering replica-exchange method for the multidimensional version.
abstract: In this article, the general formulation of the multidimensional simulated-tempering replica-exchange method is described. In previous works, the one-dimensional replica-exchange simulated-tempering and simulated-tempering replica-exchange methods were developed. For the former method, the weight factor of the one-dimensional simulated tempering is determined by a short replica-exchange simulation and multiple-histogram reweighing techniques. For the latter method, the production run is a replica-exchange simulation with a few replicas not in the canonical ensembles but in the simulated-tempering ensembles which cover wide ranges of temperature. Recently, the general formulation of the multidimensional replica-exchange simulated tempering was presented. In this article, the extension of the simulated-tempering replica-exchange method for the multidimensional version is given. As an example of applications of the algorithm, a two-dimensional replica-exchange simulation and two simulated-tempering replica-exchange simulations have been performed. Here, an alpha-helical peptide system with a model solvent has been used for the applications.
authors.affiliation: Department of Physics, Keio University, Yokohama, Kanagawa 223-8522, Japan. ayori@mail.rk.phys.keio.ac.jp
authors.forename: Ayori
authors.initials: A
authors.lastname: Mitsutake
mesh_terms: D019295:Computational Biology; D003198:Computer Simulation; D007089:Image Enhancement; D008958:Models, Molecular; D009010:Monte Carlo Method; D010455:Peptides / Q000737:chemistry; D011487:Protein Conformation; D017510:Protein Folding; D013696:Temperature
chemical_list: D010455:Peptides