The structural and energetic properties of poly(3-hexyl-thiophene) (P3HT) and 6,6-phenyl C61 butyric acid methyl ester (PCBM) monolayers and multilayers on the Ag(111) surface are investigated using classical force fields and molecular dynamics simulations. The results demonstrate that P3HT has a stronger interaction with the substrate, while PCBM exhibits larger monolayer formation energy due to stronger intermolecular interactions. In addition, PCBM prefers a “tail-up” conformation by orienting the phenyl and butyric acid methyl ester groups away from the surface, thus favoring a denser packing, while relaxation of intermolecular order in P3HT is found to initiate above 450 K. For the simulations a new parameterization of the General Amber Force Field involving dihedral angles and interactions with the Ag(111) substrate was developed. The new parameters were validated successfully against available crystal structures and ab initio data.