>I am modelling O2 molecule activation (from triplet to singlet) and the bond cleavage in oxidative enzyme as a function of different cofactors. For this purpose I generated a set of frozen O2 separations for 1.4-3.0A with a step of 0.1A (16 independent systems with frozen reaction coordinate O-O bond to 1.4, 1.5, 1.6, ... 3.0A), there is own set for each co-factor candidate. The surrounding protein environment consists of frozen root atoms bound to unconstrained side-chain fragments. I am optimizing the systems with the reaction coordinate constraint to obtain a reaction path (crossing fingers to obtain a tractable series of steps from reagents to the products). There are two questions about how to convert the series of intermediates into enzyme efficiency (as function of a cofactor).
>1. Entropy of the reaction. As the first approximation a Boltzmann distribution can be calculated for a chance to pass the reaction barrier using discrete firefly energies. Is it possible/does it make sense to softly constrain the reaction coordinate and perform a sort of random walk around each rc value (like umbrella sampling technique). Then extract entropy with a (sort of) WHAM (weighted histogram analysis) approach. Is it worst to dig in for such second order approximation or it gives next to no benefits? If the answer is positive, can you give a hint of how to activate such random walk process in firefly and what statistics is so-so sufficient to extract the entropy?
As to first part of your question, there is no way in Firefly to perform this sampling automatically. Perhaps a kind of script can be written instead.