In his workshop you will learn how to visualize and analyze single molecules, 3D volumetric data and molecular dynamics trajectories.
In his workshop you will learn how to visualize and analyze single molecules, 3D volumetric data and molecular dynamics trajectories.
| Setup | Download files required for the lesson | |
| 00:00 | 1. Using VMD on Digital Research Alliance of Canada systems |
What is VMD used for?
How to use VMD remotely on Alliance clusters? |
| 00:15 | 2. Loading Structure Files and Interacting with Molecules |
How to load PDB files into VMD?
How to view molecules interactively? How to measure distances, angles and dihedrals? |
| 00:55 | 3. A first look at the command-line interface |
How to start VMD in text mode?
How to use VMD commands? |
| 01:10 | 4. Visualizing and analyzing trajectories |
How to load structure files and trajectories into VMD?
How to animate trajectories? How to generate RMSD data from a trajectory? |
| 01:40 | 5. Visualizing Volumetric Data | How to visualize volumetric data? |
| 02:05 | 6. Scripting |
How to work with atom selections?
How to change attributes of selected atoms? How to move and superimpose selections? How to write loops How to measure distances between groups of atoms? |
| 02:45 | 7. Making movies and rendering photorealistic images |
What is Photorealistic Rendering in VMD, and how can I use it?
How to make animations? |
| 03:10 | 8. Continuum Electrostatics Calculations | How to compute and visualize electrostatic potential? |
| 03:20 | Finish |
The actual schedule may vary slightly depending on the topics and exercises chosen by the instructor.