(736h) Foyer: A Framework for Defining Force Field Usage Semantics and Atom-Typing Molecular Systems

Authors: 
McCabe, C., Vanderbilt University
Klein, C., Vanderbilt University
Sallai, J., Vanderbilt University
Summers, A. Z., Vanderbilt University
Cummings, P. T., Vanderbilt University
Iacovella, C. R., Vanderbilt University
The availability of forcefields 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 forcefields 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 a tool - Foyer [1] - that eliminates ambiguity in force field parameter usage thereby enhancing reproducibility and simplifying the process of disseminating new force fields. Foyer can serve as a standalone tool and accepts several commonly used chemical topology formats but was also designed to facilitate automated system initialization using mBuild [2]. mBuild constructs the initial configurations for systems while Foyer seamlessly parametrizes those systems upon saving to a simulation input file. To address the issues arising from rigid rule hierarchies and the segregation of force field parameters from their atom-typing tools, Foyer provides a force field agnostic method for defining parameter usage that relies upon SMARTS [3] based annotations of chemical context to perform atom-typing and thereby simplifying dissemination of force fields. In Foyer, rigid rule hierarchies are replaced by an iterative process which allows rules to be embedded in any order within the actual force field files alongside the parameter definitions, thus delivering annotations that are both human and machine readable. This also allows rules to be tested for logical consistency, independent of the chemical species they actually describe.


We present several case studies, including the development of a novel force field for perfluoropolyethers [4], that demonstrate the forcefield annotation scheme and how it can be used to simplify the process of disseminating a force field and ensuring that end users correctly use the derived parameters. Foyer has been developed as a Python library, designed to integrate with the Molecular Simulation Design Framework (MoSDeF) [5] currently under development at Vanderbilt.

  1. C. Klein, A. Z. Summers, T. Ma, C. R. Iacovella, and J. Sallai, “Foyer.” [Online]. Available: https://github.com/mosdef-hub/foyer.

  2. C. Klein, J. Sallai, T. J. Jones, C. R. Iacovella, C. McCabe, and P. T. Cummings, “A Hierarchical, Component Based Approach to Screening Properties of Soft Matter,” in Foundations of Molecular Modeling and Simulation, 2016, pp. 79–92.

  3. http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

  4. J. Black, G. Silva, C. Klein, C.R. Iacovella, P. Morgado, L. Martins, E. Filipe, C. McCabe, “ Perfluoropolyethers: Development of an All-Atom Force Field for Molecular Simulations and Validation with New Experimental Vapor Pressures and Liquid Densities”, under review

  5. https://github.com/mosdef-hub