(192bg) Mosdef, a Python-Based Molecular Simulation and Design Framework
- Conference: AIChE Annual Meeting
- Year: 2017
- Proceeding: 2017 Annual Meeting
- Group: Computational Molecular Science and Engineering Forum
- Time: Monday, October 30, 2017 - 3:15pm-4:45pm
Foyer is a general tool for applying force fields to molecular systems (i.e., atom-typing) that does not rely upon rigid rule hierarchies to atom-type a system.Â Foyer is designed such that it separates the engine that evaluates the atom-typing rules from the rules themselves, making it easier to debug, extend, and disseminate force fields.Â Foyer provides a force field and simulator agnostic schema for defining parameter usage that relies upon SMARTS  based annotations of chemical context, providing both human and machine readable documentation of parameter usage along with the parameters themselves in a single XML document.
mBuild and Foyer are able to output fully parameterized structures to various file formats used by common simulation engines (E.g. GROMACS, LAMMPS, HOOMD-Blue etc.). These tools can be coupled with the Signac-flow workflow manager , allowing large scale screening over parameter space. As such, MoSDeF provides a flexible, yet clear approach to encapsulate the routines and parameters used when initializing and performing molecular simulations. Which increases transparency and reproducibility of simulation results.
 C. Klein, J. Sallai, T. J. Jones, C. R. Iacovella, C. McCabe, and P. T. Cummings, âA Hierarchical, Component Based Approach to Screening Properties of Soft Matter,â in Foundations of Molecular Modeling and Simulation, 2016, pp. 79â92.
 Iacovella, C. R.; Sallai, J.; Klein, C.; Ma, T. In Idea Paper: Development of a Software Framework for Formalizing Forcefield Atom-Typing for Molecular Simulation, 4th Workshop on Sustainable Software for Science: Practice and Experiences (WSSSPE4), 2016.
Â C. S. Adorf and P. Dodd, âSignac-Flow.â [Online]. Available: https://bitbucket.org/glotzer/signac-flow.