Figure 1
From: Large-scale molecular dynamics simulation: Effect of polarization on thrombin-ligand binding energy
(A) Comparison of the RMSDs from two 500 ns simulations based on the AMBER force field (black) and PPC scheme (red). The average RMSD based on the PPC simulation is shown as a blue line. For comparison, the average RMSD based on the AMBER simulation is shown as a green line. (B) Distributions of the RMSDs of AMBER (black) and PPC simulations (red).
