(376am) Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems
- Conference: AIChE Annual Meeting
- Year: 2019
- Proceeding: 2019 AIChE Annual Meeting
- Group: Computational Molecular Science and Engineering Forum
- Time: Tuesday, November 12, 2019 - 3:30pm-5:00pm
Here, we present the Foyer tool [1,2,3] that eliminates ambiguity in force field parameter usage thereby enhancing reproducibility and simplifying the process of disseminating new force fields. Foyer provides a force field agnostic method for defining parameter usage and a Python based software library for evaluating these files. Foyer relies upon the OpenMM XML file format  to encode parameter usage, where this format is extended to allow the chemical context to be encoded using the SMARTS language for chemical patterns . In Foyer, rule precedence is set by âoverridesâ statements encoded in the forcefield file, rather rigid rule hierarchies, allows rules to be embedded in any order within the actual force field files, thus delivering annotations that are both human and machine readable. Rules are evaluated using an iterative process, whereby all rules are fully evaluated, allowing the force field file to be validated for completeness. Foyer has been developed to integrate with the Molecular Simulation Design Framework (MoSDeF) .
- Iacovella, C. R.; Sallai, J.; Klein, C.; Ma, T. Idea Paper : Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation. In 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4); 2016.
- Foyer [Online]. Available: https://github.com/mosdef-hub/foyer.
- Klein, C., Summers, A.Z., Thompson, M.W., Gilmer, J., McCabe, C., Cummings, P.T., Sallai, J. and Iacovella, C.R., 2018. Formalizing Atom-typing and the Dissemination of Force Fields with Foyer. arXiv preprint arXiv:1812.06779.
- OpenMM [Online]. Available: http://openmm.org