The main piece of software used in this course is VMD (Visual Molecular Dynamics). We will use this to visualize our systems and perform some basic analysis.
Additionally, any software that you are interested in running on the cluster would be best to install locally on your computer for running pieces of the tutorial that are shorter but this is not absolutely necessary as the steps can be completed on the cluster: NAMD and GROMACS.
AMBER requires a separate liscence to download and use their software not on the cluster.
Each lesson will also have assciated tutorial files that can be downloaded here.