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The interaction of proteins with biomaterials plays an important role for several biomedical applications including implants and tissue engineering. Although different experimental approaches have been explored, the investigation of the molecular models for protein-substrate interaction is warranted to control of cellular functions. In this study, Molecular Dynamics (MD) simulations were used to study the adsorption behavior of Bone Morphogenetic Protein-2 (BMP-2) on a hydrophobic graphite substrate. The influence of four different orientations of the protein with the substrate was evaluated based on their adsorption behavior. Results indicate a strong influence of the initial configuration on the adsorption. Protein unfolding was observed for most orientations with preferential binding of residues within the vicinity of the substrate. Most of the secondary structure of the protein was preserved during the simulation with a minor reduction of β-sheet structures. This research provides a detailed understanding of the interaction of BMP-2 with biomaterial surfaces.