Molecular dynamics simulations can aid studies of the structural and physicochemical properties of proteins, by predicting their dynamics, energetics, and interactions with their local environment at the atomistic level. We argue that nonstandard protocols are needed to realistically model collagen proteins, which in their biological state aggregate to form collagen fibrils, and so should not be treated as fully solvated molecules. A new modeling approach is presented that can account for the local environment of collagen molecules within a fibril and which therefore simulates aspects of their behavior that would not otherwise be distinguished. This modeling approach exploits periodic boundaries to replicate the supermolecular arrangement of collagen proteins within the fibril, in an approach that is more commonly associated with modeling crystalline solids rather than mesoscopic protein aggregates. Initial simulations show agreement with experimental observations and corroborate theories of the fibril's structure.