The use of molecular dynamics simulations can reveal fascinating details about atomic processes that are crucial to drug discovery, material science, chemistry, engineering, and fundamental research. However, learning molecular dynamics can feel overwhelming. This workshop will help you decide whether it's right for you and how to begin. We will review molecular dynamics theory and discuss practical aspects of modeling atomic interactions and simulating dynamics. The course will teach you how to prepare your initial structure, set up simulation parameters, perform molecular dynamics simulations, analyze the results, and visualize complex molecules. We will walk you through the entire molecular dynamics workflow introducing key tools and tips along the way.

Sessions:
Day 1: Practical considerations for Molecular Dynamics.
Day 2: Visualizing Structures with VMD.
Day 3: Molecular Dynamics with AMBER and NAMD.
Day 4: Analyzing Molecular Dynamics Data with PYTRAJ.  

We will be using the online programming environment Jupyter for our teaching. Your browser must be reasonably up-to-date for this to work. You can access Jupyter Hub with current versions of Chrome, Safari, and Firefox. (Some older browsers, such as Internet Explorer 9 and lower, may not be sufficient).