- Learn about computational chemistry, molecular mechanics and force-fields, and basic statistical mechanics (lectures — Find these on Canvas)
- Download and install the necessary programs and files on your Mac
- Learn the basics of VMD such as loading files and manipulating views
- Learn some intermediate topics in VMD such as making complex selections and using scripting (simple programming)
- Learn about the files needed for visualization and simulation, and how to create them
During the last week, you will work on a full simulation, from downloading, preparing, running, and analysis. It is a good idea to choose a protein from the RCSB or the class list early (during the second week?), and work with it as you do the other assignments. This page will offer some suggestions.
Syllabus