This work establishes a protocol to study via Molecular Dynamics simulation the degradation of Per-and Polyfluoroalkyl Substances (PFAS) in water by hydroxyl radical. To achieve this, molecular dynamics simulations are carried out, using ReaxFF reactive interaction potential. Simulations are carried out under a temperature ramp for determining all possible products. Using this methodology, reaction pathways of perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) are identified.