title: Multiple scaling replica exchange for the conformational sampling of biomolecules in explicit water.
abstract: A multiple scaling replica exchange method for the efficient conformational sampling of biomolecular systems in explicit solvent is presented. The method is a combination of the replica exchange with solute tempering (REST) technique and a Tsallis biasing potential. The Tsallis biasing increases the sampling efficiency, while the REST minimizes the number of replicas needed. Unbiased statistics can be obtained by reweighting of the data using a weighted histogram analysis technique. The method is illustrated by its application to a ten residue peptide in explicit water.
authors.affiliation: Center for Biological Physics and Department of Chemistry and Biochemistry, 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: D000682:Amyloid / Q000737:chemistry*; D003198:Computer Simulation; D008956:Models, Chemical; D010446:Peptide Fragments / Q000737:chemistry*; D011487:Protein Conformation; D014867:Water / Q000737:chemistry
chemical_list: D000682:Amyloid; D010446:Peptide Fragments; D014867:Water