In this paper, we illustrate a practical technique to improve the efficiency of the so-called multiple Bennett acceptance ratio (MBAR) estimator [Shirts and Chodera, J. Chem. Phys. 129, 124105 (2008)] for computing thermodynamic expectations of physical quantities, from samples drawn from Hamiltonian or temperature replica exchange simulations. The methods exploit the Crooks fluctuation theorem [Crooks, J. Stat. Phys. 90, 1481 (1998)] for accurately evaluating the partition functions ratios of neighboring replicas, thus providing an excellent initial guess for the MBAR iterative procedure.
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See supplementary material at http://dx.doi.org/10.1063/1.4821814 for an archive file containing the MBAR program and the test data used to produce Figures 1 and 2.
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