Figure 1.

Constraint topology of the original and optimized cholesterol model in Martini 2. (Left) Structural formula. (Center) Martini 2 bead representation of the original cholesterol model rendered using VMD²⁸ (gray, interacting beads carrying masses; magenta, virtual sites). (Right) Bond graph of the original and optimized models. Light and dark gray circles represent massive sites (with and without interactions, respectively), magenta circles are virtual sites in the original topology, and light pink circles are the newly introduced virtual sites (black lines, constrained bonds involving massive sites; magenta lines, constrained bonds between massive and virtual sites; blue line, flexible bond; green dashed line, flexible bond angle; red dotted line, flexible dihedral angle connecting the two constrained polyhedra, O.O.P, virtual sites out-of-plane with respect to the defining particles).