One puzzle concerning Photosystem Ⅱ(PSⅡ),a core component for photosynthesis,is that only one of the two symmetric branches in its reaction center is active in electron transfer.To investigate the effect of PSII environment on the preferential selection of the energy transfer pathway(a prerequisite for electron transfer),we have constructed an exciton model via extensive molecular dynamics simulations and quantum mechanics/molecular mechanics calculations based on a recent X-ray structure.Our results suggest that it is essential to take into account an ensemble of protein conformations in order to accurately compute the site energies.We identify the cofactor CLA606 of active chain as the most probable site for the energy excitation.We further pinpoint a number of charged protein residues that collectively lower the CLA606 site energy.Our work provides insights into understanding the molecular mechanisms of the core machinery of the green plant photosynthesis.