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

Edward Lyman, Daniel Zuckerman

Research output: Contribution to journalArticle

7 Citations (Scopus)

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.

Original languageEnglish (US)
Article number081102
JournalJournal of Chemical Physics
Volume130
Issue number8
DOIs
StatePublished - Mar 9 2009
Externally publishedYes

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switches
sampling
Switches
Sampling
simulated annealing
alanine
Simulated annealing
Alanine
peptides
Trajectories
Nuclear magnetic resonance
trajectories
Annealing
Peptides
nuclear magnetic resonance
annealing
Temperature
temperature

ASJC Scopus subject areas

  • Physics and Astronomy(all)
  • Physical and Theoretical Chemistry

Cite this

Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol. / Lyman, Edward; Zuckerman, Daniel.

In: Journal of Chemical Physics, Vol. 130, No. 8, 081102, 09.03.2009.

Research output: Contribution to journalArticle

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