Projects

Projects I have maintained and/or led development of

• mBuild - A flexible, hierarchical molecule builder written in Python.

• foyer - A package for atom-typing force fields, parametrizing molecular simulations, and disseminating force fields.

• pairing - An analysis tool that finds and analyzes molecular pairs and clusters over the course of a trajectory.

• scattering - A Python package including a set of functions that generate neutron/X-Ray scattering-style data from molecular simulation trajectories.

Other projects I have contributed to

• A handful of mBuild recipes: Pore-Builder, dropletbuilder, and Nanotube-Builder

• MDTraj - A powerful Python library for analyzing trajectories, particularly things that rely on distance calculations (RMSD, RDFs, etc.). Development has slowed in the past few years.

• ParmEd - A Python tool that converts chemical topologies across formats with excellent support for file formats used by GROMACS, OpenMM, CHARMM, and AMBER.

• MDanalysis - A Python package for analyzing trajectories, much like MDTraj but with a larger and more active community in recent years.

• signac-flow - A part of the (https://signac.io/) framework, which elegantly manages large and heterogeneous data spaces, this signac-flow handles interactions with supercomputing clusters.