Molecular dynamics simulations of VVD protein with four different configurations, native dark and native light configurations, and transient dark and transient light configurations.

(a) 2D-RMSD plot of the simulations with different configurations with reference to the native dark and light structures, respectively, (each contour in different color represents the samplings from three trajectories with the same configuration); (b) Estimated relaxation timescale based on transition probabilities among different microstates regarding with the different lag time as interval for analysis.