title: Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol.
abstract: We recently applied a multistage reweighting scheme to demonstrate the sampling of equilibrium configurational distributions of peptides from nonequilibrium, simulated annealing trajectories [E. Lyman and D. M. Zuckerman, J. Chem. Phys. 127, 065101 (2007)]. Here we demonstrate that a statistical variance reduction technique, resampling, improves the efficiency of the protocol by about a factor of 3 in a penta-alanine system. While we are not optimistic for the ultimate efficiency of purely temperature-based sampling methods, resampling-type improvements ought to find application in other (formally equivalent) nonequilibrium sampling protocols, such as Jarzynski-relation calculations and annealing-based NMR structure calculations.
authors.affiliation: Center for Biophysical Modeling and Simulation, University of Utah, 315 S 1400 E, Rm. 2020, Salt Lake City, Utah 84112-0850, USA. elyman@hec.utah.edu
authors.forename: Edward
authors.initials: E
authors.lastname: Lyman
authors.forename: Daniel M
authors.initials: DM
authors.lastname: Zuckerman
mesh_terms: D000409:Alanine / Q000737:chemistry*; D009682:Magnetic Resonance Spectroscopy; D008968:Molecular Conformation; D010455:Peptides / Q000737:chemistry*; D011487:Protein Conformation; D016008:Statistical Distributions; D013696:Temperature
chemical_list: D010455:Peptides; D000409:Alanine