Formalizing atom-typing and the dissemination of force fields with foyer
Formalizing atom-typing and the dissemination of force fields with foyer
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DOI：
10.1016/j.commatsci.2019.05.026
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发表时间：
2018-12
影响因子：
3.3
通讯作者：
Christoph Klein;Andrew Z. Summers;M. Thompson;Justin B. Gilmer;C. McCabe;P. Cummings;J. Sallai
中科院分区：
文献类型：
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作者：
Christoph Klein;Andrew Z. Summers;M. Thompson;Justin B. Gilmer;C. McCabe;P. Cummings;J. Sallai
提高分子模拟社区再现性的一个关键组成部分是减少用于进行研究的分子模型参数化的模糊性。分子模型的模糊性通常源于分子力场的使用文档不足以及力场通常不以软件直接可用的格式传播的事实。具体地，缺乏用于注释特定力场的规则的普遍适用的方案和用于执行自动参数化的通用工具（即，原子分型）可能导致不容易识别的模型参数化中的错误。在这里，我们介绍了Foyer，一个开源的Python工具，它使用户能够以人类和机器可读的格式定义和应用力场原子类型规则，并为力场传播提供了一个框架，从而消除了原子类型的模糊性并提高了可重复性。Foyer以XML格式定义力场，其中SMARTS字符串用于定义特定原子类型的化学背景，“覆盖”用于设置规则优先级，而不是严格的分层方案。在这里，我们描述了底层的方法和力场注释方案的门厅软件，展示了它的应用在几个用例，并讨论了具体方面的门厅方法，旨在提高再现性。
A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models used to perform a study. Ambiguity in molecular models often stems from inadequate usage documentation of molecular force fields and the fact that force fields are not typically disseminated in a format that is directly usable by software. Specifically, the lack of a generally applicable scheme for the annotation of the rules of a particular force field and a general purpose tool for performing automated parameterization (i.e., atom-typing) based on these rules, may lead to errors in model parameterization that are not easily identified. Here, we presentFoyer, an open-source Python tool that enables users to define and apply force field atom-typing rules in a format that is both human- and machine-readable and provides a framework for force field dissemination, thus eliminating ambiguity in atom-typing and improving reproducibility. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type and “overrides” are used to set rule precedence, rather than a rigid hierarchical scheme. Herein we describe the underlying methodology and force field annotation scheme of the Foyer software, demonstrate its application in several use-cases, and discuss specific aspects of the Foyer approach that are designed to improve reproducibility.