Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

ABSTRACT: λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased esti

SUBMITTER: Ding X 

PROVIDER: S-EPMC5828534 | biostudies-literature | 2017 Jun

REPOSITORIES: biostudies-literature