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## Abstract The weighted histogram analysis method (WHAM) has become the standard technique for the analysis of umbrella sampling simulations. In this article, we address the challenges (1) of obtaining fast and accurate solutions of the coupled nonlinear WHAM equations, (2) of quantifying the stat
The calculation of free energies by computer simulation represents one of the most promising areas in molecular modeling. While the computational methods developed so far give reliable results for liquids or solutions, they are not satisfactory for globular proteins. The reproducibility of the data
We present a comparison of four free energy calculation methods: Ε½ . Ε½ . thermodynamic integration TI ; traditional free energy perturbation FEP ; Ε½ . Bennett's acceptance ratio method IPS ; and a method that is related to an Ε½ . implementation of the WHAM method CRS . The theoretical bases of the