(1b) Mosdef: Molecular Simulation and Design Framework

We present a collection of tools designed to enable the facile setup, initialization, atom-typing, and molecular dynamics (MD) simulations, termed MoSDeF [1]. In particular, MoSDeF has been developed to enable computational MD-based screening of soft materials [2]. The core tool, mBuild [2,3], generates starting configurations by minimizing or even eliminating the need to explicitly translate and orient components when building systems - users simply state which components to connect. mBuild supports parameterized structures through generative modeling. This allows for declaratively expressing repetitive structures, e.g. polymer chains, crystal structures, planar or spatial tiling, as well as for parameterizing the affine transformations applied to subcomponents of a composite component. For end users, this minimizes and often eliminates the need to explicitly rotate and translate components when assembling systems. Additionally, the approach enables users to programmatically vary parameters for a family of systems (e.g., polymer chain length) or interchange individual components (e.g., polymer type), while still employing the same general framework. mBuild integrates with the Foyer tool for cataloging and applying force fields to molecular systems (i.e., atom-typing). Foyer provides a force field and simulator agnostic method for defining parameter usage that relies upon SMARTS [5] based annotations of chemical context, providing both human and machine readable documentation of parameter usage, which also aids in the dissemination of force fields. These tools are coupled with the Signac-flow workflow manager [6], allowing large scale screening over parameter space. Building upon prior work [2], we demonstrate the utility and flexibility of our tool chain by screening the frictional properties of several families of monolayers.

[1] 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,” in Foundations of Molecular Modeling and Simulation, 2016, pp. 79–92.

[3] https://github.com/mosdef-hub/mbuild

[4]  https://github.com/mosdef-hub/foyer

[5] http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

[6]  C. S. Adorf and P. Dodd, “Signac-Flow.” [Online]. Available: https://bitbucket.org/glotzer/signac-flow.