(376am) Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems

Authors: 
Iacovella, C. R., Vanderbilt University
Gilmer, J., Vanderbilt University
Klein, C., Vanderbilt University
Summers, A. Z., Vanderbilt University
Thompson, M., Vanderbilt University
Cummings, P. T., Vanderbilt University
McCabe, C., Vanderbilt University
Sallai, J., Vanderbilt University
Volgyesi, P., Vanderbilt University
The availability of force fields for molecular simulation has reduced the effort researchers must devote to the task of determining the interactions between species, allowing them to instead focus on the motivating scientific questions. However, determining which parameters in a forcefield to use is still often a very tedious and error prone task, given that force fields may contain hundreds of unique parameters for a single element, differentiated by the chemical context for which they apply. While tools for performing atom-typing exist (i.e., determining which parameters describe an atom’s interaction potential with its environment based on its chemical context), they are often tied to a specific force field or simulation software and typically employ a rigid hierarchy where rules that identify more specialized atom types must be called ahead of more general atom types. More importantly, many of these atom-typing tools are not directly tied to the files containing the definitions of the force field parameters, which may introduce ambiguities as to appropriate usage and the source of parameters. The strong dependence of force field parameters on the chemical context of the atoms demands a codified, logic-based expression tied directly to those parameters.

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 [4] to encode parameter usage, where this format is extended to allow the chemical context to be encoded using the SMARTS language for chemical patterns [5]. In Foyer, rule precedence is set by “overrides” 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) [6].

  1. 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.
  2. Foyer [Online]. Available: https://github.com/mosdef-hub/foyer.
  3. 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.
  4. OpenMM [Online]. Available: http://openmm.org
  5. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
  6. https://github.com/mosdef-hub