Supplementary Figure 5: States in the MSM are well equilibrated.
From: Structure-guided simulations illuminate the mechanism of ATP transport through VDAC1
Each state in the MSM was separately analyzed for internal barriers. To do this, all configurations in each state were isolated and clustered into two substates using the k-centers k-mediods algorithm. The transition probability matrix at a 5 ns lag time was constructed, and the second eigenvalue was used to identify the relaxation time between the substates according to Eq. 7. Of the 210 states in the full MSM, 187 states (89%) relaxed faster than the 5 ns lag time used to construct the full MSM (blue circles), while 23 states (11%) relaxed much slower or failed to relax at all (red circles). Dropping these later states from the MFPT analysis had little effect on the results (data not shown).
