Molecular dynamics can provide useful information for characterizing the internal motions of biomacromolecules with time. For a comparison study, the 10 ns molecular dynamics simulations were performed, respectively, for the crystal structures of PPARa (1k7l), PPARc (1k74), as well as their complexes with GW409544 and Comp#1, i.e., PPARa-GW409544, PPARc-GW409544, PPARa-Comp#1, and PPARc-Comp#1. As we can see from Fig. 3 , all the characters concerned reached the simulation equilibrium within the 5ns (see panels A and C). Meanwhile, the corresponding root mean square deviation (RMSD) value curves of the protein backbone for PPARa, PPARc, PPARa-GW409544, PPARc-GW409544, PPARa-Comp#1, and PPARc-Comp#1 were also computed, respective-ly. It is interesting to see that the RMSD curves for PPARa-Comp#1 and PPARc-Comp#1 are remarkably more stable than those of PPARa-GW409544 and PPARc-GW409544, particularly for the case of PPARa (1k7l) system, where only a fluctuation of around 0.3 nm was observed when the complex system reached the plateau.