Effects of Water Models on Binding Affinity: Evidence from All-Atom Simulation of Binding of Tamiflu to A/H5N1 Neuraminidase
Figure 3
-RMSD of wild-type NA when interacting with Tamiflu during 20 ns simulations with different combination of force fields and water models. For AMBER equilibration time ns for SPC (black arrow) while ns for remaining water models (magenta arrow). In OPLS ns for TIP3P (green arrow) and 5 ns for other models (magenta arrow). In the CHARMM case all systems reach equilibrium after about 8 ns. For GROMOS ns (black arrow) and 10 ns (red arrow) for SPC and SPC/E, respectively.
