Table 1.

Results of the MFPT calculations on alanine dipeptide solvated in water with 6 cells placed as shown on Fig. 5. Exact MFPTs were calculated by running five 68 ns long MD trajectories. The standard deviation of predicted MFPT of DiM and MD calculations are given in the brackets. For DiM, standard deviation was calculated from a single execution by using Bayesian inference (details in Appendix B). The total cost for DiM is given as a sum of the simulation time of all trajectories and the simulation time used for preparation of initial distributions.

Method	MEPT [ps], (sd [ps]) α → β/β → α	total cost [ns]
straightforward MD	66.4 (2.7)/53.8 (4.6)	68
DiM, 100 trajectories/Milestone	66.5 (11.1)/39.0 (4.6)	5.0 + 0.6 = 5.6
DiM, 250 trajectories/Milestone	57.7 (5.4)/46.5 (3.6)	12.5 + 1.0=13.5
DiM, 500 trajectories/Milestone	61.2 (4.2)/46.8 (2.6)	22.8 + 2.0=24.8
DiM, 1000 trajectories/Milestone	57.0 (2.7)/45.2 (1.8)	46.1 + 3.9=50.0
DiM, 5000 trajectories/Milestone	59.5 (1.3)/44.2(0.8)	230 + 10.1=240.1
MMVT, 0.4 ns /cell	60.2/43.9	2.4
MMVT, 0.8 ns/cell	57.2/43.7	4.8
MMVT, 1.6 ns/cell	63.2/41.2	9.6
MMVT, 3.4 ns/cell	63.4/53.2	20.4
MMVT, 12 ns/cell	62.4/48.3	72.0