Calculation of free-energy differences and potentials of mean force by a multi-energy gap method.
A method is proposed to significantly accelerate the convergence of free-energy calculations. It introduces a bias factor in Monte Carlo simulations or, equivalently, a bias force in molecular dynamics simulations. The bias factor targets the energy gap, i.e., the difference in energy function between two states, and is therefore specifically designed for calculating free-energy differences. The goal is to make the probability density of the energy gap as uniform as possible, thus allowing for its accurate determination. An iterative procedure, based on simulations at higher temperatures, is devised to obtain the bias factor. The same method naturally extends to the calculation of potentials of mean force. The generalized coordinate, for which the potential of mean force is to be calculated, now plays the role of the energy gap. Applications to model systems confirm the expected increase in accuracy of calculated free-energy differences and potentials of mean force.
Zhou
Huan-Xiang
HX
Department of Physics and Institute of Molecular Biophysics and School of Computational Science, Florida State University, Tallahassee, FL 32306, USA. zhou@sb.fsu.edu
D003198:Computer Simulation; D004735:Energy Transfer; D019277:Entropy; D006859:Hydrogen / Q000737:chemistry; D007700:Kinetics; D013816:Thermodynamics
D006859:Hydrogen