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Copyright © 2003 The Biophysical Society All rights reserved.
Biophysical Journal, Volume 85, Issue 4, 2147-2157, 1 October 2003


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Robust Biased Brownian Dynamics for Rate Constant Calculation

Gang Zou* and Robert D. SkeelGo To Corresponding Author 

* Renaissance Technologies, East Setauket, New York
Department of Computer Science and Beckman Institute, University of Illinois, Urbana, Illinois

Address reprint requests to Robert D. Skeel, 1304W. Springfield Ave., 2316 DCL, University of Illinois, Urbana, IL 61801. Tel.: 217-333-2727.


A reaction probability is required to calculate the rate constant of a diffusion-dominated reaction. Due to the complicated geometry and potentially high dimension of the reaction probability problem, it is usually solved by a Brownian dynamics simulation, also known as a random walk or path integral method, instead of solving the equivalent partial differential equation by a discretization method. Building on earlier work, this article completes the development of a robust importance sampling algorithm for Brownian dynamics—i.e., biased Brownian dynamics with weight control—to overcome the high energy and entropy barriers in biomolecular association reactions. The biased Brownian dynamics steers sampling by a bias force, and the weight control algorithm controls sampling by a target weight. This algorithm is optimal if the bias force and the target weight are constructed from the solution of the reaction probability problem. In reality, an approximate reaction probability has to be used to construct the bias force and the target weight. Thus, the performance of the algorithm depends on the quality of the approximation. Given here is a method to calculate a good approximation, which is based on the selection of a reaction coordinate and the variational formulation of the reaction probability problem. The numerically approximated reaction probability is shown by computer experiments to give a factor-of-two speedup over the use of a purely heuristic approximation. Also, the fully developed method is compared to unbiased Brownian dynamics. The tests for human superoxide dismutase, Escherichia coli superoxide dismutase, and antisweetener antibody NC6.8, show speedups of 17, 35, and 39, respectively. The test for reactions between two model proteins with orientations shows speedups of 2578 for one set of configurations and 3341 for another set of configurations.