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Zhang BW , Xia J , Tan Z , Levy RM
A Stochastic Solution to the Unbinned WHAM Equations
J Phys Chem Lett. 2015 Oct 1;6(19) :3834-40
PMID: 26722879 PMCID: PMC4894662
AbstractThe 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 "WHAMMED" 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-guest ligand binding containing approximately 3.5 x 10(7) 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.
NotesZhang, Bin W Xia, Junchao Tan, Zhiqiang Levy, Ronald M R01 GM030580/GM/NIGMS NIH HHS/United States GM30580/GM/NIGMS NIH HHS/United States Journal Article Research Support, N.I.H., Extramural Research Support, U.S. Gov't, Non-P.H.S. United States J Phys Chem Lett. 2015 Oct 1;6(19):3834-40. doi: 10.1021/acs.jpclett.5b01771. Epub 2015 Sep 14.