Fig 3. Markov state model (MSM) construction of eight macrostates based on the 300 microstates generated using k-means clustering analysis of VVD MD simulations.

(a) Plot of 300 microstates on 2D RMSD surface belonging to eight macrostates with different colors representing different macrostates; (b) Distribution of each macrostate on the 2D RMSD surface; (c) Representative structures of eight macrostates.