Molecular dynamics simulations and quantum chemistry calculations have been combined to describe the dark adaptation in bacteriorhodopsin (bR). The process involves the reversible thermally activated transformation of retinal from an all-trans to a 13-cis,15-syn configuration. The potential surface governing the thermal isomerization of retinal around two (13-14, 15-N) double bonds has been determined for representative protein configurations taken from molecular dynamics trajectories. CASSCF(8,8)/6-31G level ab initio calculations (within Gaussian94) were carried out for this purpose. The charge distributions of all atoms in the protein are represented by partial point charges and explicitly included in the electronic Hamiltonian. Placement of retinal into bR is found to reduce the calculated isomerization barrier. Thermal fluctuations of the protein lead to a further effective reduction of this barrier. The isomerization process is shown to be catalyzed by the protonation of an aspartic acid (Asp85) side group of bacteriorhodopsin.