分子模拟的人类学习：VMD中的集合变量仪表板
Human learning for molecular simulations: the Collective Variables Dashboard in VMD
摘要：
Collective Variables Dashboard是一个软件工具，用于在可定制的集体变量空间中实时、无缝地探索分子结构和轨迹。仪表板源于集体变量模块与可视化软件VMD的集成，并增加了一个完全可扩展的图形界面，为集体变量的设计和分析提供交互式工作流程。典型的用例包括用于增强采样和自由能模拟的集合变量的先验设计，以及对集合变量空间中任何类型的模拟或结构集合的事后分析。这些情况的组合通常发生在初步模拟时，有偏见或无偏见，揭示了一组优化的集体变量是必要的，以改善进一步模拟中的采样。然后，仪表板提供了一种高效的方式，可以直观地探索可能的集体变量的空间，在现有数据上验证它们，并使用集体变量模块在进一步的偏置模拟中直接使用所产生的集体变量定义。我们说明了两个应用程序上的仪表板的使用：发现坐标来描述配体从蛋白质结合位点解结合，并设计基于体积的变量来偏置跨膜孔的水合作用。
英文摘要：
The Collective Variables Dashboard is a software tool for real-time, seamless exploration of molecular structures and trajectories in a customizable space of collective variables. The Dashboard arises from the integration of the Collective Variables Module with the visualization software VMD, augmented with a fully discoverable graphical interface offering interactive workflows for the design and analysis of collective variables. Typical use cases include a priori design of collective variables for enhanced sampling and free energy simulations as well as post-mortem analysis of any type of simulation or collection of structures in a collective variable space. A combination of those cases commonly occurs when preliminary simulations, biased or unbiased, reveal that an optimized set of collective variables is necessary to improve sampling in further simulations. Then the Dashboard provides an efficient way to intuitively explore the space of likely collective variables, validate them on existing data, and use the resulting collective variable definitions directly in further biased simulations using the Collective Variables Module. We illustrate the use of the Dashboard on two applications: discovering coordinates to describe ligand unbinding from a protein binding site, and designing volume-based variables to bias the hydration of a transmembrane pore.
机构、总结、中文摘要均由AI分析而来，可能存在错误，请以论文正文为准。
