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Huber GA, McCammon JA. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010;181(11):1896-1905doi: 10.1016/j.cpc.2010.07.022.
Huber, G. A., & McCammon, J. A. (2010). Browndye: A Software Package for Brownian Dynamics. Computer physics communications, 181(11), 1896-1905. https://doi.org/10.1016/j.cpc.2010.07.022
Huber, Gary A, and McCammon, J Andrew. "Browndye: A Software Package for Brownian Dynamics." Computer physics communications vol. 181,11 (2010): 1896-1905. doi: https://doi.org/10.1016/j.cpc.2010.07.022
Huber GA, McCammon JA. Browndye: A Software Package for Brownian Dynamics. Comput Phys Commun. 2010 Nov 01;181(11):1896-1905. doi: 10.1016/j.cpc.2010.07.022. PMID: 21132109; PMCID: PMC2994412.
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Comput Phys Commun. 2010 Nov 01;181(11):1896-1905. doi: 10.1016/j.cpc.2010.07.022.

Browndye: A Software Package for Brownian Dynamics.

Computer physics communications

Gary A Huber, J Andrew McCammon

Affiliations

  1. Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093-0365.

PMID: 21132109 PMCID: PMC2994412 DOI: 10.1016/j.cpc.2010.07.022

Abstract

A new software package, Browndye, is presented for simulating the diffusional encounter of two large biological molecules. It can be used to estimate second-order rate constants and encounter probabilities, and to explore reaction trajectories. Browndye builds upon previous knowledge and algorithms from software packages such as UHBD, SDA, and Macrodox, while implementing algorithms that scale to larger systems.

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