Figure 6.

RMSD of the ligand heavy atoms compared to the reference binding mode. The RMSD is plotted as a function of simulation time for the unbiased MD simulations of the cluster representatives. A preceding fit to the protein backbone, but not to the ligand coordinates was performed. (a) Histamine in complex with the H₁ receptor, (b) adrenaline, and (c) alprenolol both in complex with the ${\beta }_2$ adrenoceptor. The arrow in panel (a) marks the rapid increase of the histamine RMSD of cluster 5 due to the dissociation of the ligand from the receptor.