Free energy methods in molecular simulation

An overview is given of methods for calculating free energies by molecular simulation. Techniques may be categorized as density-of-states methods and work-based methods. Emphasis is given to the latter, with particular focus on issues of performance and accuracy. Two points of view are provided for understanding these issues. One is based on the distribution of work values observed in the calculation, and the other considers the relationship of the important regions of phase space for the systems. We present a metric that brings together the two viewpoints, and provide a demonstration that connects to the accuracy of a calculation as a function of sampling length. We also discuss staging methods and their appropriate formulation in consideration of phase-space relations.