The effect of the initial atoms distribution on the molecular dynamics (MD) simulation of a model atomic fluid (argon) is investigated for the case of the isochoric phase transition to the supercritical state. In particular, the case of uniformly distributed atoms in the simulation domain is compared with the case of separated liquid and vapor atoms. The sensitivity of simulations to asymmetric nanoscale perturbations in the boundary is also studied. Despite its high computational cost, the MD approach has the potential to successfully address long‐standing problems in computational fluid dynamics (CFD), especially those associated with mathematical singularities, such as contact angles, vortices, phase transitions and so forth. Unlike conventional CFD simulations, where the initial condition is the pressure or velocity distribution in the simulation domain, MD simulations also require the initial position of each molecule. Thus, it is important to understand whether a judicious choice of the initial distribution of molecules can reduce the overall computation time of the simulation. The evolution of the model fluid system during the phase transition was simulated using a Lennard‐Jones interatomic potential, corrected with the Lorentz–Berthelot mixing rule for the interactions with the solid walls. The system was allowed to relax until equilibrium, and then a Heaviside temperature step was applied to the wall to bring the system to supercritical conditions. Results show the initial choice of the atoms distribution can significantly affect the computational time, while the effect of asymmetric perturbations on the boundary is negligible.