(342w) The Molecular Simulation Design Framework (MoSDeF): New Features to Improve User Experience and Support Reproducible Molecular Simulations

The Molecular Simulation Design Framework (MoSDeF) is a suite of Python libraries containing routines necessary for the programmatic and reproducible initialization of chemical systems for molecular simulation, with a major focus on molecular dynamics (MD) and Monte Carlo (MC) simulations[1]. This project is driven by our efforts to encourage and support TRUE (Transparent, Reproducible, Usable by others, Extensible) simulations as discussed by Thompson et al. [2]. Of the three major libraries in the MoSDeF suite, two of them, mBuild [3, 4] and Foyer [5, 6], have been used in numerous scientific projects to date [7-9]. As part of our continuing development of the MoSDeF tools, these two libraries have undergone major improvements over the past year to assist with the construction of chemical systems. For example, mBuild now incorporates RDKit to generate molecules from SMILES strings, providing better control and improved reproducibility of the system initialization process. The Foyer library has undergone major refactoring, supporting atom-typing and parameterization of generic graph structures. These changes make Foyer a more versatile tool, now supporting a wider range of input formats. A new backend data structure has been integrated called the General Molecular Simulation Object (GMSO)[10], which stores topological information for chemical systems and their interaction parameters. The GMSO library was designed with minimal assumptions about the type of chemical systems to be supported, as well as symbolic mathematics support for the many potential energy functional forms found in common force fields. This enables GMSO to support a wide range of systems, from small molecule organic liquids, to coarse-grained systems, crystalline structures, and others. All packages in the MoSDeF software suite follow software development best practices, which includes detailed documentation of implemented functions, unit testing and Continuous Integration (CI). The MoSDeF tools listed above are all available on conda-forge and installed using the Conda scientific software package manager.

References

1. MoSDeF: https://github.com/mosdef-­hub.
2. M. W. Thompson, Justin B. Gilmer, Ray A. Matsumoto, Co D. Quach, Parashara Shamaprasad, Alexander H. Yang, Christopher R. Iacovella, Clare McCabe & Peter T. Cummings (2020) Towards molecular simulations that are transparent, reproducible, usable by others, and extensible (TRUE), Molecular Physics, 118:9-10.
3. 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, 79-92.
4. mBuild: https://github.com/mosdef-­hub/mbuild.
5. C. Klein, A. Z. Summers, M. W. Thompson, J. B. Gilmer, C. McCabe, P. T. Cummings, Janos Sallai, Christopher R. Iacovella. “Formalizing atom-typing and the dissemination of force fields with foyer”, Computational Materials Science, Volume 167, 2019. https://doi.org/10.1016/j.commatsci.2019.05.026.
6. https://github.com/mosdef-­hub/foyer.
7. A. Z. Summers, C. R. Iacovella, P. T. Cummings, and C. McCabe. “Investigating Alkylsilane Monolayer Tribology at a Single-Asperity Contact with Molecular Dynamics Simulation”. Langmuir 2017 33 (42), 11270-11280. DOI: 10.1021/acs.langmuir.7b02479
8. A. Z. Summers, J. B. Gilmer, C. R. Iacovella, P. T. Cummings, and C. McCabe. “MoSDeF, a Python Framework Enabling Large-Scale Computational Screening of Soft Matter: Application to Chemistry-Property Relationships in Lubricating Monolayer Films”. Journal of Chemical Theory and Computation 2020 16 (3), 1779-1793. DOI: 10.1021/acs.jctc.9b01183.
9. N. C. Craven, J. B. Gilmer, C. J. Spindel, A. Z. Summers, C. R. Iacovella, and C. McCabe , "Examining the self-assembly of patchy alkane-grafted silica nanoparticles using molecular simulation" , The Journal of Chemical Physics 154, 034903 (2021) https://doi.org/10.1063/5.0032658
10. GMSO: https://github.com/mosdef-hub/gmso.