Restraints There are different ways to apply restraints during MD:
- Positional Restraints (Tethering to Original Positions) This method tethers distal regions of the protein or system to their original coordinates. It is useful when you want those parts to remain relatively static in absolute space—for example, anchoring terminal residues or regions far from the ligand. This is the option in the GUI or you can use the option -rl in runMDopenMM script
- Internal Restraints ( Ca=Ca Distance Restraints) This method restrains internal geometry-such as keeping the distance between alpha carbons (Ca) of key residues. It allows the system to move globally but helps preserve the relative structure of specific elements (e.g., loops or helices).
- Select the region of the 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.