(189au) MoSDeF: A Python-Based Molecular Simulation and Design Framework

Authors: 
Gilmer, J., Vanderbilt University
Klein, C., Vanderbilt University
Sallai, J., Vanderbilt University
Summers, A. Z., Vanderbilt University
Iacovella, C., Vanderbilt University
Lédeczi, Á., Vanderbilt University
Volgyesi, P., Vanderbilt University
Cummings, P. T., Vanderbilt University
McCabe, C., Vanderbilt University
The Molecular Simulation and Design Framework (MoSDeF) [1] is an extensible set of Python tools focused on designing chemical systems, atom typing, and screening over large sets of such systems in a programmatic fashion. MoSDeF has been developed as an effort to improve the current state of reproducibility within the molecular simulation community. Currently, MoSDeF is built around two key pieces of software, mBuild [2,3] for designing systems of interest, and foyer [4,5] for applying the appropriate force fields to a molecular system. mBuild supports a wide range of systems due to the robust particle connection method used and ability to declaratively express repetitious structures with small amounts of code. This leads to parameterization of many features of a system, for example, from terminal group chemistry of a polymer chain, basis particles within a crystal lattice, size and composition of a nanoparticle, and much more. Foyer allows for atom typing of molecular systems and does not rely on rigid, hard-coded, rule hierarchies for atom type application. By separating the engine that applies the force field from the force field file itself, the atom typing process can be debugged much easier, force fields can more easily be extended, evolved, and disseminated with publications. Additionally, in combination with the workflow management tool Signac-flow [6], MoSDeF allows for large-scale screening capabilities, while also maintaining reproducibility and human-readability.

References

[1] “MoSDeF” [Online]. Available: https://github.com/mosdef-­hub.

[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”, Foundations of Molecular Modeling and Simulation, 2016, pp. 79-92.

[3] “mBuild” [Online]. Available: https://github.com/mosdef-­hub/mbuild.

[4] 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.

[5] “foyer” [Online]. Available: https://github.com/mosdef-­hub/foyer.

[6] “Signac-flow” [Online]. Available: https://bitbucket.org/glotzer/signac-flow.