SI2-SSE: Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation

分子模拟在理解原子和分子水平的相互作用方面起着关键作用，这些相互作用是许多自然和人造材料和过程的基础。经典的分子模拟依赖于力场来描述存在于原子和/或原子群之间的各种相互作用。分子模拟力场的可用性减少了研究人员必须投入到确定物种之间相互作用的困难和昂贵的任务上的努力，使他们能够专注于激励的科学问题。然而，确定使用力场中的哪些参数仍然是一项繁琐且容易出错的任务。这种困难与参数对原子的化学环境的强烈依赖有关；化学环境可能取决于分子中原子的局部键合环境，邻近原子的局部环境，所考虑的分子类型，分子的相等。力场可以包含数十或数百种不同类型的相同元素，其中每种类型代表不同化学环境中的元素。Atom类型可能具有挑战性，通常需要用户查阅分散在参数文件中的文本注释或发布参数的科学文献。不幸的是，到目前为止，典型力场的文档往往是稀缺和非结构化的，通常用简单的英语或特别的速记符号表示，导致歧义和增加错误使用的可能性。虽然有一些免费的工具可以帮助进行原子类型化，但这些工具通常是特定于特定力场或模拟器的，并且以难以维护、调试和发展的方式捕获原子类型化和参数化规则。该项目的中心原则是，研究社区迫切需要一种与力场无关的形式体系，以一种足以供人类使用的表达方式来表达原子类型和参数化规则，同时是机器可读的，以便在复杂的科学工作流程中实现自动化。这项工作建议建立一种形式来表达特定力场参数适用的化学背景（即，力场使用语义），并建立一个原子类型工具来解释这种形式以生成可证明正确的力场参数化。用这种形式注释力场将作为原子类型和参数使用的清晰、明确的文档，并且还允许在开发过程中以编程方式确定力场规范中的歧义或不一致。成功地开发这个框架将简化原子分型所需的规则，随着力场的不断增长、专门化和变得更加复杂，这一点至关重要。机器可读的力场使用语义注释将使繁琐和容易出错的任务自动化，并有可能实现新的应用领域，从自动化力场比较和交叉验证，到集成多个力场和模拟器工具的复杂仿真工作流程。将开发一个开放的在线力场存储库，其中包含标注的力场、相关的开源软件以及如何在拟议框架内使用、标注和开发力场的文档，以传播结果并促进社区参与。

Molecular simulation plays a key role in understanding the atomistic and molecular level interactions that underlie many natural and man-made materials and processes. Classical molecular simulations rely upon forcefields to describe the various interactions that exist between atoms and/or groups of atoms. The availability of forcefields for molecular simulation has reduced the effort researchers must devote to the difficult and costly task of determining the interactions between species, allowing them to instead focus on the motivating scientific questions. However, determining which parameters in a forcefield to use is still often a tedious and error prone task. This difficulty is related to the strong dependence of the parameters on the chemical context of the atoms; the chemical context may depend on the local bonded environment of an atom in a molecule, the local environment of neighboring atoms, the type of molecule(s) being considered, the phase of the molecule(s), etc. Forcefields can contain tens or hundreds of different types of the same element, where each type represents the element in a different chemical context. Atom typing can be challenging, often requiring the user to consult textual comments scattered in parameter files or the scientific literature where the parameters were published. Unfortunately, as of today, the documentation of a typical forcefield tends to be scarce and unstructured, commonly expressed in plain English or in an ad-hoc shorthand notation, leading to ambiguities and increasing the likelihood of incorrect usage. While there are freely available tools to aid in atom-typing, these are typically specific to a particular forcefield or simulator and capture the atom-typing and parameterization rules in ways that are hard to maintain, debug, and evolve. The central tenet of this project is that there is an imminent need in the research community for a forcefield agnostic formalism to express atom-typing and parameterization rules in a way that is expressive enough for human consumption, while being machine readable to enable automation in complex scientific workflows. This work proposes to establish a formalism to express the chemical context for which a particular forcefield parameter is applicable (i.e., forcefield usage semantics) and an atom-typing tool that interprets this formalism to generate forcefield parameterizations that are provably correct. Annotating forcefields with this formalism will serve as clear, unambiguous documentation of the atom-types and parameter usage, and also allows ambiguities or inconsistencies in forcefield specifications to be programmatically pinpointed during development. Successfully developing this framework will simplify the rules needed for atom-typing, which is crucial as forcefields continue to grow, specialize, and become more complex. The machine-readable annotations of forcefield usage semantics will enable automating tedious and error prone tasks and have the potential to enable new application areas, ranging from automated forcefield comparison and cross-validation, to complex simulation workflows integrating multiple forcefields and simulator tools.   An open online forcefield repository containing the annotated forcefields, associated open source software, and documentation on how to use, annotate, and develop forcefields within the proposed framework will be developed to disseminate results and foster community involvement.