TY - JOUR
T1 - Formalizing atom-typing and the dissemination of force fields with foyer
AU - Klein, Christoph
AU - Summers, Andrew Z.
AU - Thompson, Matthew W.
AU - Gilmer, Justin B.
AU - McCabe, Clare
AU - Cummings, Peter T.
AU - Sallai, Janos
AU - Iacovella, Christopher R.
N1 - Funding Information:
This material is based upon work supported by the National Science Foundation under Grants 535150 and 1835874 . We also acknowledge the National Energy Research Supercomputing Center, which is supported by the Office of Science of the U.S. Department of Energy under Contract No. DE-AC02-05CH11231.
Publisher Copyright:
© 2019 Elsevier B.V.
PY - 2019/9
Y1 - 2019/9
N2 - 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.
AB - 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.
KW - Force fields
KW - Molecular simulation
KW - Open-source software
KW - Reproducibility
UR - http://www.scopus.com/inward/record.url?scp=85066294701&partnerID=8YFLogxK
U2 - 10.1016/j.commatsci.2019.05.026
DO - 10.1016/j.commatsci.2019.05.026
M3 - Article
AN - SCOPUS:85066294701
SN - 0927-0256
VL - 167
SP - 215
EP - 227
JO - Computational Materials Science
JF - Computational Materials Science
ER -