HOOMD-blue

HOOMD-blue is a general-purpose particle simulation toolkit. It scales from a single CPU core to thousands of GPUs.
You define particle initial conditions and interactions in a high-level python script. Then tell HOOMD-blue how you want to execute the job and it takes care of the rest. Python job scripts give you unlimited flexibility to create custom initialization routines, control simulation parameters, and perform in situ analysis.

Download and get started using HOOMD-blue today.

Freud

Freud is an analysis software package meant for the analysis of molecular dynamics and Monte Carlo simulation trajectories. Freud works with and returns NumPy arrays. Freud is system independent and is able to process both 2D and 3D data. It consists of functionalities such as computing radial distribution function, local density, hexagonal order parameter and local bond order parameters.
Some ipython-notebook examples can be found here: Freud examples.

Signac

The Signac framework aids in the management of large and heterogeneous data spaces.
It provides a simple and robust data model to create a well-defined indexable storage layout for data and metadata. This makes it easier to operate on large data spaces, streamlines post-processing and analysis and makes data collectively accessible.
signac is open-source and freely available for Python versions 2.7.x and 3.4+.
For more details about Signac and how to get started please visit the Signac website.