A Stochastic Solution to the Unbinned WHAM Equations

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• 作者：Bin W. Zhang ; Junchao Xia ; Zhiqiang Tan ; Ronald M. Levy
• 刊名：The Journal of Physical Chemistry Letters
• 出版年：2015
• 出版时间：October 1, 2015
• 年：2015
• 卷：6
• 期：19
• 页码：3834-3840
• 全文大小：412K
• ISSN：1948-7185

文摘

The weighted histogram analysis method (WHAM) and unbinned versions such as the multistate Bennett acceptance ratio (MBAR) and unbinned WHAM (UWHAM) are widely used to compute free energies and expectations from data generated by independent or coupled parallel simulations. Here we introduce a replica exchange-like algorithm (RE-SWHAM) that can be used to solve the UWHAM equations stochastically. This method is capable of analyzing large data sets generated by hundreds or even thousands of parallel simulations that are too large to be 鈥淲HAMMED鈥?using standard methods. We illustrate the method by applying it to obtain free energy weights for each of the 240 states in a simulation of host鈥揼uest ligand binding containing 鈭?.5 脳 10⁷ data elements collected from 16 parallel Hamiltonian replica exchange simulations, performed at 15 temperatures. In addition to using much less memory, RE-SWHAM showed a nearly 80-fold improvement in computational time compared with UWHAM.