In order to learn how to deal with 3D coordinates in the context of a MD program we study a very simple system: Two C atoms connected by a bond. The bond is modelled as a harmonic force. In Assignment 04 you derived the analytical form of a harmonic force between two particles. You can use this to code the force routine that is used to integrate the equations of motion of the two body system. Use hoscmd_v0.py as basis.
mdIO.py contains updated functions for writing XYZ trajectories, which can then be viewed.
VMD is a versatile molecular visualization program. It is very good at displaying MD trajectories and is geared towards biopolymers and liquids but it can be used for a wide range of systems.
On the Macs, you will find it in /Applications.