The distribution of activation energies for ligand rebinding in conformational substates of sperm whale myoglobin is investigated with a molecular dynamics-quenching method. The technique approximately locates transition states for curve crossing processes using an interpolating Hamiltonian as in Marcus’s electron transfer theory. Linear free energy relations are examined. The transition from the dissociated state to the activated state involves a collective motion of the protein. The activation energy is correlated more to the extent of the collective motion of the protein than to the change of any single bond or bond angle. The predicted average structures of fast and slow rebinding substates which will soon be accessible to determination by cryogenic X-ray crystallography are compared. The CO geometry of the activated protein complex from the simulation agrees well with the structure of a low temperature photodissociated intermediate determined by Schlichting et al.