布朗染料：一个用于布朗动力学的软件包。
Browndye: A Software Package for Brownian Dynamics.
作者信息
Huber Gary A, McCammon J Andrew
机构信息
Howard Hughes Medical Institute, University of California San Diego, La Jolla, CA 92093-0365.
出版信息
Comput Phys Commun. 2010 Nov 1;181(11):1896-1905. 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.
摘要
我们推出了一款名为Browndye的新软件包，用于模拟两个大型生物分子的扩散相遇过程。它可用于估计二阶速率常数和相遇概率，并探索反应轨迹。Browndye基于诸如UHBD、SDA和Macrodox等软件包的先前知识和算法构建，同时实现了可扩展到更大系统的算法。
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