If we wish to use the MBAR free energy estimator, we must calculate the energies of samples obtained at a given value of λ at all other values of λ. Protocols which adaptively change the number of λ-windows according to Equation 18 are then inconvenient because of the need to compute energies at all values of λ at which may be used. This can result in a substantial overhead. Therefore, we select λ values to achieve minimum variance using Equation 19 based on a short set of initial simulations of negligible cost. σ ∂H ∂λ was determined as a function of λ for a default set of windows using a single replicate run with 0.1 ns sampling per window. This is effectively equivalent to selecting states to achieve equal and sufficient overlap when statistical inefficiency is ignored. We then adaptively allocate simulation time to achieve minimum standard error of the mean according to Equation .