Practical Aspects of Free-Energy Calculations: A Review

作者：Niels Hansen, Wilfred F. van Gunsteren · 发表于：Journal of Chemical Theory and Computation · 年份：2014 · DOI：10.1021/ct500161f · 被引用次数：396 · 研究领域：Protein Structure and Dynamics、Advanced Chemical Physics Studies、Spectroscopy and Quantum Chemical Studies

Free-energy calculations in the framework of classical molecular dynamics simulations are nowadays used in a wide range of research areas including solvation thermodynamics, molecular recognition, and protein folding. The basic components of a free-energy calculation, that is, a suitable model Hamiltonian, a sampling protocol, and an estimator for the free energy, are independent of the specific application. However, the attention that one has to pay to these components depends considerably on the specific application. Here, we review six different areas of application and discuss the relative importance of the three main components to provide the reader with an organigram and to make nonexperts aware of the many pitfalls present in free energy calculations.