VMD Workshop - Advanced Class

10:00 - 11:30 Basics of Tcl and the core VMD commands

• Work through the handout from the Welch book
• I'll explain how VMD works with Tcl
• The vector and matrix extensions will be covered
• We'll go through the VMD commands at http://www.ks.uiuc.edu/Research/vmd/ug/node74.html
• I doubt we'll have time to get to this VMDTech

11:30-12:00 Ways to configure VMD

1:15-2:00 Making movies

• Go over some of the the different rendering methods
• Basics of making a movie from a script
• The "take_picture" script

2:00-2:30 User-defined graphics

2:45-3:45 Molecular analysis commands

• The molinfo command
• The atomselect command.
• Plot the center of mass of retinal over time, and print the distance traveled for each step. Source.

3:45-4:05 Using "trace"