Multiple Bennett acceptance ratio made easy for replica exchange simulations

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. (C) 2013 AIP Publishing LLC.