Transition path sampling parameters

Transition Path Sampling Methods 367 4.1 Reaction Coordinate vs. Order Parameter... 

Fig. 13. In an umbrella sampling simulation for pathways configuration space is covered with a sequence of overlapping windows W[i]. For each window a separate transition path sampling simulation for paths with starting points in A and endpoints in >V[ ] is carried out. From the order parameter distributions matched where the windows overlap the distribution PA X,t) can be calculated...

The exact results shown in previous paragraphs are obtained by using the analytical calculation under the hypothesis that the transition rate matrix M of Markov process is available. But in practical application, this assumption is not always true. Assume now that the M is unknown and that only available data are a single sample path of Markov process. Since the realistic data set of this trajectory is not available here, it need to be simulated with parameter values given in Table 1. The goal is to use the perturbation analysis technique to estimate the DlM s measures mentioned above from this data set. In fact, the simulation is made for 100000 transitions. 

---