title: Replica-exchange method in van der Waals radius space: overcoming steric restrictions for biomolecules.
abstract: We present a new type of the Hamiltonian replica-exchange method, where the van der Waals radius parameter and not the temperature is exchanged. By decreasing the van der Waals radii, which control spatial sizes of atoms, this Hamiltonian replica-exchange method overcomes the steric restrictions and energy barriers. Furthermore, the simulation based on this method escapes from the local-minimum free-energy states and realizes effective sampling in the conformational space. We applied this method to an alanine dipeptide in aqueous solution and showed the effectiveness of the method by comparing the results with those obtained from the conventional canonical and replica-exchange methods.
authors.affiliation: Department of Physics, School of Science, Nagoya University, Nagoya, Aichi 464-8602, Japan. itoh@tb.phys.nagoya-u.ac.jp
authors.forename: Satoru G
authors.initials: SG
authors.lastname: Itoh
authors.forename: Hisashi
authors.initials: H
authors.lastname: Okumura
authors.forename: Yuko
authors.initials: Y
authors.lastname: Okamoto
mesh_terms: D004151:Dipeptides / Q000737:chemistry; D056004:Molecular Dynamics Simulation; D011487:Protein Conformation; D015203:Reproducibility of Results; D013696:Temperature; D013816:Thermodynamics; D014867:Water / Q000737:chemistry
chemical_list: D004151:Dipeptides; D014867:Water; C002956:alanylalanine