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We present an efficient method to compute transition rates between states fora two-state system. The method utilizes the equivalence between steady-stateflux and mean first passage rate for such systems. More specifically, theprocedure divides the configurational space into smaller regions andequilibrates trajectories within each region efficiently. The equilibratedconditional probabilities between each pair of regions lead to transition ratesbetween the two states. We apply the procedure to a non-trivial coarse-grainedmodel of a 70 residue section of the calcium binding protein, calmodulin. Theprocedure yields a significant increase in efficiency compared to brute-forcesimulations, and this efficiency increases dramatically with a decrease intemperature.

Biomolecular transitions: efficient computation of pathways, free energies, and rates