Nano fluids are very suitable for enhancing heat transfer in electronics cooling systems. Exploring the behavior of thermo physical properties of these fluids helps us to use them in various industrial applications. Different theories have been proposed so far to predict the properties of nanofluid. However, there are many inconsistencies in these studies, which have been done experimentally, numerically, and theoretically. These discrepancies in results persuade us to use molecular dynamics simulations for understanding the behavior of nanofluids properties since drastical changes in the physical properties of the base fluid by the nano particles can be described in the molecular interaction scales. In this project, the stability problem and thermal conductivity of nanofluid were investigated using the molecular dynamics simulation method. The results showed that the addition of nanoparticles to the base fluid with a volume fraction of 1.15 % increase the thermal conductivity of nanofluid by 12.8 % compared to the base fluid. Also, by increasing the volume fraction of nanofluid to 5.78 percent, thermal conductivity increases by 38 percent compared to the base fluid. The results show aggregation of nanoparticles increases the thermal conductivity of nanofluid by 22 percent compared to the base fluid. Moreover, covering the nanoparticles with one type of silane coupling agent improves the stability of the nano fluid, but on the other hand, it reduces the thermal conductivity of nanofluid compared to non-coated nanofluid and increases only 5 % of the thermal conductivity compared to the base fluid. Keywords: nanofluids, molecular dynamics, thermal conductivity, stability of nanofluids, polymer coating, non equilibrium, aggregation of nanoparticle