The Dashboard window

The Dashboard window displays a table listing currently defined variables, and their values for the current frame indicated at the bottom of the window. By default the frame is updated to track VMD's currently displayed frame, but that can be changed by toggling the ``Track frame'' checkbox, e.g. to animate the trajectory without recomputing expensive variables. Vector-values variables can be expanded to list their scalar elements. This is necessary when individual scalar quantities have to be selected for plotting. Other operations act on variables as a whole and ignore specific selected scalar elements.

Buttons above the table allow for general operations on the state of the Colvars Module. Buttons below the table offer operations on selected variables.

If several molecules are loaded, the dashboard only interacts with the molecule labeled "top" (T in VMD's main window). If the top molecule is changed, the Colvars Module needs to be reset using the Reset button. This will remove all current definitions, so make sure to save the variables to a file beforehand.

If variables are modified, added or deleted interactively or by an external script, hit ``Refresh'' or press F5 to update the displayed variables and values. Starting the dashboard also enables trajectory animation using the left/right arrow keys within VMD's graphical window. Atomic coordinates can be modified using VMD's ``Mouse/Move'' functions, and the Colvars Module can then be updated by pressing F5 directly from the graphical window.

A dropdown list allows for changing the current unit system if no variables are defined. If some variables are already defined, it is recommended to edit the configuration for all of them at once (eg. pressing Ctrl-a, then Ctrl-e), checking that all quantities are expressed in the desired set of units, and adding the units keyword to the general parameters, outside of colvar {} blocks ().

Another dropdown lets the user change which VMD molecule is associated with the Colvars module. Internally, this requires recording the configuration of currently defined colvars, deleting the current instance of the Colvars module, creating a new one linked to the target molecule, and applying the saved configuration. Beware of incompatible colvar definitions, such as atom groups listing atom IDs that exist in one molecule, but not the other. Auto-updating selections (see below) can be used to adapt the colvar definitions to a different system using VMD selection texts.