  We provide an introduction to molecular dynamics simulations in the context
of the Kob-Andersen model of a glass. We introduce a complete set of tools for
doing and analyzing the results of simulations at fixed NVE and NVT. The
modular format of the paper allows readers to select sections that meet their
needs. We start with an introduction to molecular dynamics independent of the
programming language, followed by introductions to an implementation using
Python and then the freely available open source software package LAMMPS. We
also describe analysis tools for the quick testing of the program during its
development and compute the radial distribution function and the mean square
displacement using both Python and LAMMPS.
