The photoisomerization of the retinylidene chromophore and the process of thermal relaxation of its strained conformation were examined by restrained molecular dynamic simulations in the transmembrane model of rhodopsin. This model was constructed based on the projection map obtained by electron cryomicroscopy. The photoconversion process from the 11-cis-retinylidene chromophore to the all-trans chromophore was traced by simultaneous rotation of the adjacent C12-C13 bond, leading to an all-trans chromophore having a C11-C12-twisted and C12-C13-s-cis conformation for the bathorhodopsin chromophore. In accord with the characteristic CD signals at 500 and 540 nm, the retinylidene chromophore of rhodopsin and bathorhodopsin showed characteristic right-handed and left-handed helical conformations, respectively. Subsequent rotation of the C12-C13 bond led to the lumirhodopsin chromophore with an all-trans C12-C13-s-trans conformation, affecting the backbone structure of transmembrane helix 3 by steric interaction between the 13-Me group of the chromophore and opsin. The conformational change of the chromophore from lumirhodopsin to metarhodopsin I placed the beta-ionyl portion of the chromophore in an alternate binding site and the protonated Schiff base in a position appropriate for proton transfer to its counterion, Glu113. Estimation of UV absorption of the rhodopsin and photoactivated rhodopsin chromophores indicated the importance of the PSB-Glu113 carboxylate distance, the twist of the C11-C12 double bond, and the C12-C13 s-cis conformation of the 11,13-diene portion to the bathochromic shift of bathorhodopsin.