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Bacteriorhodopsin (bR) and halorhodopsin (hR) are membrane proteins of halobacteria. Both utilize the same chromophore, all-trans retinal protonated Schiff base (RPSB), for photo-activated ion transport. In spite of their structural similarities, the photoisomerization of RPSB in bR is much faster and with higher quantum yield compared to hR. Here, we couple a QM/MM approach with ab initio multiple...