title: Efficiency of alchemical free energy simulations. I. A practical comparison of the exponential formula, thermodynamic integration, and Bennett's acceptance ratio method.
abstract: We investigate the relative efficiency of thermodynamic integration, three variants of the exponential formula, also referred to as thermodynamic perturbation, and Bennett's acceptance ratio method to compute relative and absolute solvation free energy differences. Our primary goal is the development of efficient protocols that are robust in practice. We focus on minimizing the number of unphysical intermediate states (λ-states) required for the computation of accurate and precise free energy differences. Several indicators are presented which help decide when additional λ-states are necessary. In all tests Bennett's acceptance ratio method required the least number of λ-states, closely followed by the "double-wide" variant of the exponential formula. Use of the exponential formula in only strict "forward" or "backward" mode was not found to be competitive. Similarly, the performance of thermodynamic integration in terms of efficiency was rather poor. We show that this is caused by the use of the trapezoidal rule as method of numerical quadrature. A systematic study focusing on the optimization of thermodynamic integration is presented in a companion paper.
authors.affiliation: Department of Computational Biological Chemistry, University of Vienna, Vienna, Austria.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bruckner
authors.forename: Stefan
authors.initials: S
authors.lastname: Boresch
mesh_terms: D056004:Molecular Dynamics Simulation; D013816:Thermodynamics