This tutorial demonstrates code which ties together mbuild and openbabel's SMILES/SMARTS matching to help create coarse-grain chemical structures. The tutorial also demonstrates how to initialize these coarse-grain structures in a HOOMD simulation using foyer and analyze the output of the simulation using freud.
To read more about how using simple models and community-driven, open-source tools can help lower cognitive load, increase simulation transferability, reproducibility, usability, and extensibility (TRUE), and make the world a better place, please read our perspective paper.
This tutorial depends heavily on tools from MoSDeF and the Glotzer group.