FIG. 3.
A schematic drawing of trajectory fragments initiated at milestone α. Backward trajectories in time (dashed lines) are used to assess if the trajectories are sampled from FHPD. The red dashed trajectory re-crosses the initial milestone α before hitting milestone β. Therefore, it is not sampled from FHPD. The green trajectory hits milestone β before any other milestone and is sampled from FHPD. Note that the forward trajectories (black lines) are allowed to re-cross the initial milestone before they finally terminate at a nearby milestone. The forward trajectories illustrate the operation of the transition matrix K that takes phase space points from one milestone and transmits them with certain probability to phase space points at another milestone. For Milestoning calculations, we also record the time length of the forward trajectory fragments (black lines). It is possible to exploit the identity of the terminating milestones of the backward trajectories (dashed lines) as well, but so far we have not done so. The final termination points of the trajectories (for example, the black circle at milestone β) are used as starting points for the next iteration of the flux .