Abstract
An enhanced sampling method-biased Brownian dynamics-is developed for the calculation of diffusion-limited biomolecular association reaction rates with high energy or entropy barriers. Biased Brownian dynamics introduces a biasing force in addition to the electrostatic force between the reactants, and it associates a probability weight with each trajectory. A simulation loses weight when movement is along the biasing force and gains weight when movement is against the biasing force. The sampling of trajectories is then biased, but the sampling is unbiased when the trajectory outcomes are multiplied by their weights. With a suitable choice of the biasing force, more reacted trajectories are sampled. As a consequence, the variance of the estimate is reduced. In our test case, biased Brownian dynamics gives a sevenfold improvement in central processing unit (CPU) time with the choice of a simple centripetal biasing force.
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Selected References
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- Huber G. A., Kim S. Weighted-ensemble Brownian dynamics simulations for protein association reactions. Biophys J. 1996 Jan;70(1):97–110. doi: 10.1016/S0006-3495(96)79552-8. [DOI] [PMC free article] [PubMed] [Google Scholar]