Though Python is a very popular and powerful environment for Biomolecular Simulation, many important and well-established tools require working from the command line in a terminal window. So it's an advantage to be familiar and comfortable with both ways of working.

This workshop demonstrates two approaches to running MD simulations on a simple protein system:

1. From the command line in a terminal window, using AMBER
2. In Python, via a Jupter Notebook, using OpenMM

The focus is on the preliminary simulations that are required to relax and equiliobrate an initially-built system, so that later "production" simulations have the best chance of being stable and reliable.