Software for Building a Community-Based Molecular Modeling Capability Around the Molecular Simulation Design Framework (MoSDeF)

Single slide for presentation at NSF CSSI PI meeting in Seattle, WA, February 13-14, 2020Molecular simulation plays an important role in many sub-fields of science and engineering. Systems composed of soft matter are ubiquitous in science and engineering, but molecular simulations of such systems pose particular computational challenges since the differences in potential energy between distant configurations are on the same order as the thermal motion, requiring time and/or ensemble-averaged data to be collected over long simulation trajectories for property evaluation. Furthermore, performing a molecular simulation of a soft matter system involves multiple steps, which have traditionally been performed by researchers in a ``bespoke’' fashion. The result is that many soft matter simulations are not reproducible based on the information provided in a publication, and large-scale screening of soft materials systems is a formidable challenge. To address the issues of reproducibility and computational screening capability, we have been developing the Molecular Simulation and Design Framework (MoSDeF) software suite. We also propose a set of principles to render molecular simulations Transparent, Reproducible, Usable by others, and Extensible (TRUE). While it is not required to use MoSDeF to create TRUE simulations, MoSDeF facilitates the publication and dissemination of TRUE simulations by automating many of the critical steps in performing molecular simulations, thus enhancing their reproducibility.