Photosystem II (PSII) is one of the key protein complexes in photosynthesis. We introduce a coarse grained model of PSII and present the analysis of 60 mu s molecular dynamics simulations of PSII in both monomeric and dimeric form, embedded in a thylakoid membrane model that reflects its native lipid composition. We describe in detail the setup :of the protein complex and the many natural cofactors and characterize their mobility. Overall we find that the protein subunits and cofactors are more flexible toward the periphery of the complex as well as near the PLQ exchange cavity and at the dimer interface. Of all cofactors, beta-carotenes show the highest mobility. Some of the beta-carotenes,diffuse in and out of the protein complex via the thylakoid membrane. In contrast with the PSII dimer, the monomeric form adopts a tilted conformation in the membrane, with strong interactions between the soluble PsbO subunit and the glycolipid headgroups. Interestingly, the tilted conformation causes buckling of the membrane. Together, our results provide an unprecedented view of PSII dynamics on a microsecond time scale. Our data may be used as basis for the interpretation of experimental data as well as for theoretical models describing exciton energy transfer.