Journal of Chemical Physics 2009-02-28

Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol.

Edward Lyman, Daniel M Zuckerman

Index: J. Chem. Phys. 130 , 081102, (2009)

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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.