Introduction to VMD

9:15-10:45 Loading and viewing molecules

Basic loading and viewing
• Introduction to VMD menus
• Loading files
• The various representations
• Coloring methods
• Hands-on tutorial

Advanced viewing
• Multiple renderings, atom selection, changing colors
• Display options (orthographic/perspective, clipping planes, detail levels styles, transparency)
• Picking
• Experiment
• Saving your session

10:45-11:00 Coffee Break

11:00-12:00 Animation, picking, and rendering

Animation and picking
• (Re)load the the bR PDB file)
• Append a DCD file / the Edit form
• Play around with the animation menu
• H-bonds representation and "within" syntax
• Follow the animation tutorial
• Picking bonds, angles and dihedral
• Graph picked geometries through time
• Hands-on learning

Multiple molecules, RMSD & Fitting
• VMD can display multiple molecules, load alanin.pdb
• Explain the concepts of Fixed, Drawn, and Top in VMD; delete alanin.pdb
• Go to the last frame of the DCD.
• Load another version of the bR PDB file; color both by molecule
• Do an RMSD Fit between the two bRs and print
• Follow the tutorial

Rendering
• Snapshot and how to quickly get hardcopy output
• Raster3D output
• POV3, Radiance and VRML
• Follow tutorial

12:00-1:00 Lunch break

1:00-2:15 The VMD Command Language

• Why use it?
• What is Tcl? How does it work with VMD?
• Overview of Tcl
• Overview of some of the VMD core commands
• Personalization
• Making movies
• User-defined graphics

2:15-2:30 Coffee Break

2:30-3:30 Using VMD for Molecular Analysis

• The molinfo command
• The atomselect command
• Center of mass information over time [Source]
• other examples

3:30-5:00 Open Lab Time