Open source software
I am the lead developer of HOOMD-blue, an open-source Molecular Dynamics simulation code. HOOMD-blue utilizes GPUs to greatly accelelerate simulation performance with every step of the simulation implemented in NVIDIA CUDA.
HOOMD-blue is a versatile simulation code with many available features which can be enabled and configured via simple python scripts. You can find much more information at the HOOMD-blue homepage where you can download source and/or binaries, read the documentation, and find out how you can contribute.
In house / closed source
Freud is one of many internal tools utilized by the Glotzer group. It is a hybrid C++/python library for analyzing MD trajectories (such as those written by HOOMD-blue). It provides easy access to trajectory data stored in binary dump files via a simple python interface and fast analysis of that data in highly tuned C++ routines. Standard analysis methods used in soft matter simulation research are provided.