Molecular dynamics simulation was used to investigate the structure of the H₂O molecule and its dynamical behaviour near an HIV (3LPU protein). This study simulated the atomic interaction between 3LPU protein and H₂O molecules using a precise atomic arrangement. The interaction between 3LPU protein and H₂O molecules is influenced by temperature and pressure. According to our simulated findings, the amplitude of atomic oscillation increases as the atom's temperature rises to 400 K. As a result of this occurrence, the interatomic force of structures increases. As a result, as the temperature rises, the diffusion coefficient of H₂O molecules into 3LPU protein changes from 0.421 to 0.861 μm²/ms. The dynamical behaviour of atomic structures is also influenced by pressure. The diffusion coefficient of H₂O molecules into the 3LPU protein structure fell from 0.587 to 0.052 μm²/ms when the pressure of the simulated structures was increased from 0 to 4 bar.