Efficient use of nonequilibrium measurement to estimate free energy differences for molecular systems.
A promising method for calculating free energy differences DeltaF is to generate nonequilibrium data via "fast-growth" simulations or by experiments--and then use Jarzynski's equality. However, a difficulty with using Jarzynski's equality is that DeltaF estimates converge very slowly and unreliably due to the nonlinear nature of the calculation--thus requiring large, costly data sets. The purpose of the work presented here is to determine the best estimate for DeltaF given a (finite) set of work values previously generated by simulation or experiment. Exploiting statistical properties of Jarzynski's equality, we present two fully automated analyses of nonequilibrium data from a toy model, and various simulated molecular systems. Both schemes remove at least several k(B)T of bias from DeltaF estimates, compared to direct application of Jarzynski's equality, for modest sized data sets (100 work values), in all tested systems. Results from one of the new methods suggest that good estimates of DeltaF can be obtained using 5-40-fold less data than was previously possible. Extending previous work, the new results exploit the systematic behavior of bias due to finite sample size. A key innovation is better use of the more statistically reliable information available from the raw data.
Ytreberg
F Marty
FM
Center for Computational Biology and Bioinformatics, University of Pittsburgh, 200 Lothrop St., Pittsburgh, Pennsylvania 15261, USA. dmz@ccbb.pitt.edu
Zuckerman
Daniel M
DM
D000465:Algorithms; D003198:Computer Simulation; D004735:Energy Transfer; D008962:Models, Theoretical; D013816:Thermodynamics