# msmtools.flux.rate¶

msmtools.flux.rate(totflux, pi, qminus)

Transition rate for reaction A to B.

Parameters: totflux (float) – The total flux between reactant and product pi ((M,) ndarray) – Stationary distribution qminus ((M,) ndarray) – Backward comittor kAB – The reaction rate (per time step of the Markov chain) float

committor(), total_flux(), flux_matrix()

Notes

Computation of the rate relies on discrete transition path theory (TPT). The transition rate, i.e. the total number of reaction events per time step, is given in [1] as:

$k_{AB}=\frac{1}{F} \sum_i \pi_i q_i^{(-)}$

$$F$$ is the total flux for the transition from $$A$$ to $$B$$.

References

 [1] F. Noe, Ch. Schuette, E. Vanden-Eijnden, L. Reich and T. Weikl: Constructing the Full Ensemble of Folding Pathways from Short Off-Equilibrium Simulations. Proc. Natl. Acad. Sci. USA, 106, 19011-19016 (2009)