I wrote this tutorial while I was a graduate student at the Interfacial Molecular Science Laboratory (IMSL) for the undergraduate interns who would join our lab. Their internship was often their first exposure to simulation techniques or even UNIX/Linux systems, so these material assume zero working knowledge of technical computing.

The tutorial material is highly specific to the software and computing environment we had at the lab, but some budding materials science researcher may find the introduction interesting nonetheless. This tutorial could also be easily converted to use an open-source MD code such as LAMMPS; all the same principles would apply even though the syntax is different.

What follows below and in subsequent pages are the tutorial materials as they were written in 2012.

This tutorial is aimed to equip the new researcher with the basics of working with the molecular dynamics code and related research tools used at the Interfacial Molecular Science Laboratory at Rutgers. It is a general procedure that has been put to new students for decades and provides hands-on experience in configuring and running molecular dynamics simulations.