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

SI2-SSE：开发用于分子模拟的力场原子分型形式化的软件框架

• 批准号: 1535150
• 负责人: Christopher Iacovella
• 金额: $ 50.18万
• 依托单位: Vanderbilt University
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2015
• 资助国家: 美国
• 起止时间: 2015-09-01 至 2019-08-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1535150&HistoricalAwards=false
• 关键词: SI2; SSE; Development; Software; Framework

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.

分子模拟在理解许多天然和人造材料和过程背后的原子和分子水平相互作用方面发挥着关键作用，经典分子模拟依赖于力场来描述原子和/或原子团之间存在的各种相互作用。用于分子模拟的力场减少了研究人员必须投入的确定物种之间相互作用的艰巨且昂贵的任务，使他们能够专注于激发科学问题。然而，确定要使用力场中的哪些参数通常仍然是一个难题。乏味这种困难与参数对原子化学背景的强烈依赖性有关；化学背景可能取决于分子中原子的局部键合环境、相邻原子的局部环境、类型。所考虑的分子的类型、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。 ，经常要求用户查阅文本不幸的是，截至目前，典型力场的文档往往稀缺且非结构化，通常用简单的英语或临时速记符号来表达。虽然有免费的工具可以帮助原子类型化，但这些工具通常特定于特定的力场或模拟器，并且以难以维护的方式捕获原子类型化和参数化规则，该项目的中心宗旨是，研究界迫切需要一种与力场无关的形式主义，以一种足以满足人类消费的方式表达原子类型和参数化规则，同时又是机器可读的。这项工作建议建立一种形式主义来表达特定力场参数适用的化学背景（即力场使用语义）以及解释这种形式主义的原子打字工具。生成可证明正确的力场参数化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查明力场规范中的模糊性或不一致之处。将简化原子打字所需的规则，随着力场的不断发展、专业化并变得更加复杂，这至关重要。力场的机器可读注释。使用语义将实现繁琐且容易出错的任务的自动化，并有可能实现新的应用领域，从自动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模拟工作流程​包含带注释的在线力场存储库。将开发力场、相关开源软件以及有关如何在拟议框架内使用、注释和开发力场的文档，以传播结果并促进社区参与。