Figure 1.

Rare conformational transitions in MD simulation. A schematized very long MD trajectory which successfully transitions to basin B after starting in A is superimposed over energy contours (grey lines). By definition, every unbiased transition trajectory consists of (i) a dwell period (blue) of duration t_dwell prior to the last exit from the initial state and (ii) the transition event itself (red) of duration t_b. If t_b ≪ t_dwell, then path sampling strategies may be useful in focusing computational effort on the transition process.