Transition path sampling sequences

The basis of the transition path sampling method is the statistical description of dynamical pathways in terms of a probability distribution. To define such a distribution consider a molecular system evolving in time and imagine that we take snapshots of this system at regularly spaced times fj separated by the time step At. Each of these snapshots, or states, consists of a complete description z of the system in terms of the positions q = <71, <72, , [Pg.252]

Since pathways collected with transition path sampling are true dynamical trajectories rather than artificial sequences of states such as minimum energy pathways, they can be used to study the kinetics of the reaction. In the following we will first define reaction rate constants and explain how they are related... 

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...

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