Module: Observables ()

Description:

This module is used to display information about a molecular trajectory. All properties stored in the trajectory can be displayed, e.g., potential energy, kinetic energy, total energy etc.

Connections:

Data [required]
The molecular trajectory for which properties should be displayed.

Time [optional]
A time object that may be connected to the module in order to synchronize, e.g., a viewing module with the line in the plot window, indicating the position of the time step within the trajectory.

Ports:

Option

The two options allow you to specify which kind of value, root mean square deviation (rmsd) or some observable value, should be displayed. The observable type needs to be further specified by the Observable port.

Alignment

The three ports above specify how the molecules are transformed before computing the rmsd value. See the description in the general section on alignment of molecules for a detailed explanation.

Plotting

Action

Plot the Observable Type within a new window.

Plot Option

Select the first toggle if the values of the plotted properties at the current time are shown in the plot window. If the second option is selected, only a single plot will be shown, and changing the Observable Type will update the current plot.

Time

This port is most useful in conjunction with a viewing module in order to see the property of the displayed time step. In order to create a time object, click the Time slider with the right mouse button and select Create time from the menu. As a result a time object will appear in the Project View, which should be connected with an object of type Molecule which can be visualized with, for example, the Molecule View module.