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A mini-tutorial

Here are the steps for a quick first tour of the Dashboard:

  1. load an MD trajectory into VMD;
  2. open the Dashboard;
  3. click ``New'' to create a new collective variable;
  4. in the Editor window, click ``Apply'' to accept the dein the Dashboard window, fault template;
  5. in the Dashboard window, click ``Show atoms'' to display the two atom groups involved in this distance coordinate;
  6. click ``Timeline plot'';
  7. click anywhere in the timeline plot to navigate in the trajectory.

Now, clicking ``Edit'' in the Dashboard window, you can modify the collective variable to reflect interesting geometric properties of the system. The power of the collective variables approach lies in the variety of geometric functions (``components'') and their combinations. The editor window provides a number of helpers to make it easy and quick to define the most relevant variables. See section [*] for details.