Papers › Formalizing Atom-typing and the Dissemination of Force Fields with Foyer
Formalizing Atom-typing and the Dissemination of Force Fields with Foyer
Christoph Klein, Andrew Z. Summers, Matthew W. Thompson, Justin Gilmer, Clare McCabe, Peter T. Cummings, Janos Sallai, Christopher R. Iacovella
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A key component to enhancing reproducibility in the molecular simulation community is reducing ambiguity in the parameterization of molecular models. Ambiguity in molecular models often stems from the dissemination of molecular force fields in a format that is not directly usable or is ambiguously documented via a non-machine readable mechanism. Specifically, the lack of a general tool for performing automated atom-typing under the rules of a particular force field facilitates errors in model parameterization that may go unnoticed if other researchers are unable reproduce this process. Here, we present Foyer, a Python tool that enables users to define force field atom-typing rules in a format that is both machine- and human-readable thus eliminating ambiguity in atom-typing and additionally providing a framework for force field dissemination. Foyer defines force fields in an XML format, where SMARTS strings are used to define the chemical context of a particular atom type. Herein we describe the underlying methodology of the Foyer package, highlighting its advantages over typical atom-typing approaches and demonstrate is application in several use-cases.
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