We present the BOCS toolkit as a suite of open source software tools for parametrizing bottom-up coarse-grained (CG) models to accurately reproduce structural and thermodynamic properties of high-resolution models. The BOCS toolkit complements available software packages by providing robust implementations of both the multiscale coarse-graining (MS-CG) force-matching method and also the generalized-Yvon–Born–Green (g-YBG) method. The g-YBG method allows one to analyze and to calculate MS-CG potentials in terms of structural correlations. Additionally, the BOCS toolkit implements an extended ensemble framework for optimizing the transferability of bottom-up potentials, as well as a self-consistent pressure-matching method for accurately modeling the pressure equation of state for homogeneous systems. We illustrate these capabilities by parametrizing transferable potentials for CG models that accurately model the structure, pressure, and compressibility of liquid alkane systems and by quantifying the role of many-body correlations in determining the calculated pair potential for a one-site CG model of liquid methanol.

中文翻译：

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BOCS：自底向上开源粗粒度软件

我们将BOCS工具包作为一组开源软件工具提供，用于对自下而上的粗粒度（CG）模型进行参数化，以准确地再现高分辨率模型的结构和热力学性质。BOCS工具包通过提供多尺度粗粒度（MS-CG）力匹配方法和广义Yvon-Born-Green（g-YBG）方法的可靠实现来补充可用的软件包。g-YBG方法允许人们根据结构相关性分析和计算MS-CG电位。此外，BOCS工具包实现了扩展的集成框架，用于优化自下而上的电势的可传递性，以及用于为均匀系统精确建模状态压力方程的自洽压力匹配方法。