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Harmonic distance restraints are extremely useful tools for fine-tuning your system when needed. They apply a spring-like force (with a user-defined force constant) between two atoms. In other words, the atoms are free to move in space, but their movement is constrained by a defined distance criterion.
To apply harmonic distance restraints, follow these steps:
Select two atoms using the picking mode (#1 and #2).
Open the 'Picking' popup menu, and choose the 'Add Harmonic Restraint' option.
A new window will appear, where you should specify the equilibrium distance and the force constant (Figure1).
You can add as many harmonic restraints as needed.
Figure 1: Selecting Atoms in Picking Mode and Accessing the Auxiliary Window for Applying Harmonic Distance Restrictions
When a restraint is active, it is represented in the GL area by a dashed line. You can activate or deactivate these restraints in the "Selections and Constraints" window, as shown in Figure 2. This window can be accessed from the "Selection" menu in the main window.
Figure 2: Restraints are represented by dashed lines and can be deactivated in the "Selections and Constraints" auxiliary window located in the upper-right corner of the image.
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