Figure 1.

Visualization of the setup for a QM/MM simulation. (A) The molecule of interest, a protease- substrate complex, is centered in a water filled cubic box. Both molecules are depicted with their surface in orange. (B) The MD or MM simulation box shows the protease in ribbon representation (orange), the substrate as ball-and-stick model (green), and the counterions Na⁺ (purple) and Cl⁻ as spheres. (C) Most atoms of the protease in ribbon representation were omitted for clarity, while the QM region with the substrate and the catalytic residues, displayed as ball-and-sticks, is defined by a surrounding, transparent surface. The MM–QM interface requires a special treatment, e.g., by using link atoms.