Formalizing atom-typing and the dissemination of force fields with foyer

Christoph Klein, Andrew Z. Summers, Matthew W. Thompson, Justin B. Gilmer, Clare McCabe, Peter T. Cummings, Janos Sallai, Christopher R. Iacovella*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

21 Citations (Scopus)

Abstract

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 present Foyer, 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.

Original languageEnglish
Pages (from-to)215-227
Number of pages13
JournalComputational Materials Science
Volume167
DOIs
Publication statusPublished - Sep 2019

Keywords

  • Force fields
  • Molecular simulation
  • Open-source software
  • Reproducibility

ASJC Scopus subject areas

  • Computer Science(all)
  • Chemistry(all)
  • Materials Science(all)
  • Mechanics of Materials
  • Physics and Astronomy(all)
  • Computational Mathematics

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