Figure 2.

Molecular mechanics/coarse grained (MM/CG) simulation setup. Water molecules, the extracellular part of the receptor and the ligand (in orange) constitute the all atom (MM) region, whereas the intracellular part of the receptor (in green) is the CG region. The interface (in violet) mediates the interaction between the MM and the CG regions. Carbon atoms in the atomistic and in the interface regions are coloured according to the region they belong to, whereas hydrogen atoms are in white, nitrogen in blue and oxygen in red. The potentials used to mimic the presence of the membrane and to cap the water molecules are represented as colored lines (blue, gray and yellow, respectively).