- 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)
- Read about force-fields and other fundamental topics
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
CONVENTION: things you type in the terminal or tkcon are in RED. Output from the terminal, tkcon or vmd are in BLUE.