GeomBD3 is a robust Brownian dynamics simulation package designed to easily handle natural or engineered systems in diverse environments and arrangements. The software package described herein allows users to design, execute, and analyze BD simulations. The simulations use all-atom, rigid molecular models that diffuse according to overdamped Langevin dynamics and interact through electrostatic, Lennard-Jones, and ligand desolvation potentials. The program automatically calculates molecular association rates, surface residence times, and association statistics for any number of user-defined association criteria. Users can also extract molecular association pathways, diffusion coefficients, intermolecular interaction energies, intermolecular contact probability maps, and more using the provided supplementary analysis scripts. We detail the use of the package from start to finish and apply it to a protein–ligand system and a large nucleic acid biosensor. GeomBD3 provides a versatile tool for researchers from various disciplines that can aid in rational design of engineered systems or play an explanatory role as a complement to experiments. GeomBD version 3 is available on our website at http://chemcha-gpu0.ucr.edu/geombd3/ and KBbox at https://kbbox.h-its.org/toolbox/methods/molecular-simulation/geombd/.

中文翻译：

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GeomBD3：用于生物和工程系统的布朗动力学模拟软件

GeomBD3 是一个强大的布朗动力学模拟包，旨在轻松处理各种环境和布置中的自然或工程系统。本文描述的软件包允许用户设计、执行和分析 BD 模拟。模拟使用全原子、刚性分子模型，这些模型根据过阻尼朗之万动力学进行扩散，并通过静电、Lennard-Jones 和配体去溶剂化电位相互作用。该程序自动计算任意数量的用户定义的关联标准的分子关联率、表面停留时间和关联统计。用户还可以使用提供的补充分析脚本提取分子关联途径、扩散系数、分子间相互作用能、分子间接触概率图等。我们从头到尾详细介绍了该软件包的使用，并将其应用于蛋白质-配体系统和大型核酸生物传感器。GeomBD3 为来自不同学科的研究人员提供了一个多功能工具，可以帮助工程系统的合理设计或作为实验的补充发挥解释性作用。GeomBD 版本 3 可在我们的网站 http://chemcha-gpu0.ucr.edu/geombd3/ 和 KBbox 上 https://kbbox.h-its.org/toolbox/methods/molecular-simulation/geombd/ 获得。