Theory classes: Classical dynamics at finite temperature (Hamilton equations, atomic potentials for proteins, how to introduce thermal baths). Preparation for hands-on classes: the sander module of AMBERTOOLS (what type of systems it can simulate, what type of simulations it can do, how thermal baths can be represented, input and output files). The cpptraj module of AMBERTOOLS to analyze results. Hands-on classes: How to login in and submit AMBERTOOLS jobs to Oblivion. Submit a short molecular dynamics job to Oblivion using the sander module. Inspection of the output files. Use the cpptraj module to further analyze the results. Use the software VMD to visualize proteins and protein trajectories.