Free energy computations by minimization of Kullback-Leibler divergence: An efficient adaptive biasing potential method for sparse representations

JOURNAL OF COMPUTATIONAL PHYSICS

卷:231

Article

Bilionis, I.²  Koutsourelakis, P. S.¹ 

[1] Heriot Watt Univ, Edinburgh EH14 4AS, Midlothian, Scotland

[2] Cornell Univ, Ctr Appl Math, Ithaca, NY 14853 USA

关键词: Free energy computations;    Adaptive biasing potential;    Sequential Monte Carlo;    Atomistic simulations;    Statistical learning;   

DOI  :  10.1016/j.jcp.2012.01.033

来源: Elsevier

【 摘 要 】

The present paper proposes an adaptive biasing potential technique for the computation of free energy landscapes. It is motivated by statistical learning arguments and unifies the tasks of biasing the molecular dynamics to escape free energy wells and estimating the free energy function, under the same objective of minimizing the Kullback-Leibler divergence between appropriately selected densities. It offers rigorous convergence diagnostics even though history dependent, non-Markovian dynamics are employed. It makes use of a greedy optimization scheme in order to obtain sparse representations of the free energy function which can be particularly useful in multidimensional cases. It employs embarrassingly parallelizable sampling schemes that are based on adaptive Sequential Monte Carlo and can be readily coupled with legacy molecular dynamics simulators. The sequential nature of the learning and sampling scheme enables the efficient calculation of free energy functions parametrized by the temperature. The characteristics and capabilities of the proposed method are demonstrated in three numerical examples. (C) 2012 Elsevier Inc. All rights reserved.

【 授权许可】

Free