TY - JOUR
T1 - Resampling improves the efficiency of a "fast-switch" equilibrium sampling protocol
AU - Lyman, Edward
AU - Zuckerman, Daniel M.
N1 - Funding Information:
We thank Radford Neal for comments on our previous work and Andrew Petersen for reading the present report. Support for this work was provided by the NSF (Grant No. MCB-0643456) and the NIH (GM076569).
PY - 2009
Y1 - 2009
N2 - 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.
AB - 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.
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U2 - 10.1063/1.3081626
DO - 10.1063/1.3081626
M3 - Article
C2 - 19256587
AN - SCOPUS:61449195371
SN - 0021-9606
VL - 130
JO - Journal of Chemical Physics
JF - Journal of Chemical Physics
IS - 8
M1 - 081102
ER -