Cosolvent molecular dynamics (MDs) are an increasingly popular form of simulations where small molecule cosolvents are added to water-solvated protein systems. These simulations can perform diverse target characterization tasks, including cryptic and allosteric pocket identification and pharmacophore profiling and supplement suites of enhanced sampling methods to explore protein conformational landscapes. The behavior of these systems is tied to the cosolvents used, so the ability to define diverse and complex mixtures is critical in dictating the outcome of the simulations. However, existing methods for preparing cosolvent simulations only support a limited number of predefined cosolvents and concentrations. Here, we present CosolvKit, a tool for the preparation and analysis of systems composed of user-defined cosolvents and concentrations. This tool is modular, supporting the creation of files for multiple MD engines, as well as direct access to OpenMM simulations, and offering access to a variety of generalizable small-molecule force fields. To the best of our knowledge, CosolvKit represents the first generalized approach for the construction of these simulations.

中文翻译：

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CosolvKit：用于助溶剂 MD 制备和分析的通用工具


助溶剂分子动力学 （MD） 是一种越来越流行的模拟形式，其中小分子助溶剂被添加到水溶剂化蛋白质系统中。这些模拟可以执行不同的靶标表征任务，包括隐蔽和变构的口袋鉴定和药效团分析，并补充增强采样方法套件以探索蛋白质构象景观。这些系统的行为与所使用的助溶剂有关，因此定义各种复杂混合物的能力对于决定模拟结果至关重要。但是，用于制备助溶剂模拟的现有方法仅支持有限数量的预定义助溶剂和浓度。在这里，我们介绍了 CosolvKit，这是一种用于制备和分析由用户定义的助溶剂和浓度组成的系统的工具。该工具是模块化的，支持为多个 MD 引擎创建文件，以及直接访问 OpenMM 仿真，并提供对各种可推广小分子力场的访问。据我们所知，CosolvKit 代表了构建这些模拟的第一个通用方法。