msmbuilder.cfep.CutCoordinate.evaluate_partition_functions

CutCoordinate.evaluate_partition_functions()

Computes the partition function of the cut-based free energy profile based on transition network and reaction coordinate.

Employs an MSM to do so, thus taking input in the form of a discrete state space and the observed dynamics in that space (assignments). Further, one can provide a “reaction coordiante” who’s values will be employed to find the min-cut/max-flow coordinate describing dynamics on that space.

Generously contributed by Sergei Krivov Optimizations and modifications due to TJL

See also

optimize_cut_based_coordinate

function Optimize a flexible reaction coordinate to maximize the free energy barrier along that coordinate.