To add restraints:

• Make a copy of the protein you wish to simulate - right click on the name of the protein in the ICM workspace (left hand side) and choose the option 'clone'.
• Select the region of the cloned molecule you wish to restrain and convert that selection to an 'orange' selection as described here.
• Go to MolMechaics/Run MD Simulation as described above and choose the selection in the Restrain dialog box.
• Click OK to run the simulation.