Large scale molecular dynamics (MD) simulations are performed to study the oxidation of Highly Oriented Pyrolytic Graphite (HOPG) by hyperthermal atomic oxygen beam (5eV). The simulations are performed using a classical reactive force field (ReaxFF) initially parameterized to accurately model hydrocarbon oxidation reactions. The MD simulations are compared to molecular beam experiments and good qualitative agreement is found. The simulations predict a cylindrical etch pit clearly observed in the experiments. The simulations demonstrate that oxidation is rapid and primarily occurs around defects in the graphene sheets. It is observed that the number of carbons atoms removed scales linearly with the number of oxygen atoms striking the etch pit. Furthermore, the simulations show an increase in oxidation as the surface temperature is increased. The qualitative agreement between MD simulations and experiment is encouraging and suggests that the interatomic potential used and oxidation simulation methodology described in this article are accurate and could potentially be used to study more complex surface oxidation processes relevant to hypersonic flight vehicles.