Abstract
The H2O molecule structure and its dynamical behavior around an HIV (3LPT protein) have been examined by molecular dynamics simulation. In this work, the atomic interaction between 3LPT protein and H2O molecules with precise atomic arrangement has been simulated. Radial distribution function analysis around the virus revealed two peaks of H2O molecules: a sharp one at 1.3 Å around 3LPT atoms and a broad one at 3.4 Å around protein atoms. The temperature and pressure of atomic structures affected these calculated peaks. Furthermore, these 2 parameters (Temperature and pressure) have an important effect on 3LPT protein and H2O molecules interaction. Our simulation results show that increasing the atom's temperatures to 370 K causes an increase in the amplitude of atomic oscillation. Therefore this phenomenon leads to an increase in the interatomic force of structures. So, temperature increasing causes changing the diffusion coefficient from 0.74 to 0.91 μm2/s in H2O molecules into 3LPT protein. Pressure also has a significant effect on the dynamical behavior of atomic structures. By increasing the pressure of simulated structures from 0 to 4 bar, the diffusion coefficient of H2O molecules into 3LPT protein structure increased from 0.74 to 0.84 μm2/s.
•H2O molecules structure and its dynamical behavior around a HIV virus have been examined.•Radial distribution function analysis around the virus revealed two peaks of H2O molecules.•By increasing the atoms temperatures the interatomic force raises.•Pressure also has a similar effect on the behavior of molecules dynamical manner.•By increasing pressure, the diffusion coefficient increased.