In the numerical studies of active particles, models consisting of a solid body and a fluid body have been well established and widely used. In this work, such an active Brownian particle (ABP) is realized in molecular dynamics (MD) simulations. Immersed in a fluid, each ABP consists of a head particle and a spherical phantom region of fluid where the flagellum of a microswimmer takes effect. Quantitative control over the orientational persistence time is achieved via an external stochastic dynamics. This control makes it possible to validate ABP’s diffusion property in a wide range of particle activity. In molecular description, the axial velocity of ABP exhibits a Gaussian distribution. Its mean value defines the active velocity which increases with the active force linearly, but shows no dependence on the rotational diffusion coefficient. For the active diffusion coefficient measured in free space, it shows semi-quantitative agreement with the analytical result predicted by a minimal ABP model. Furthermore, the active diffusion coefficient is also calculated by performing a quantitative analysis on the ABP’s distribution along x axis in a confinement potential. Comparing the active diffusion coefficients in the above two cases (in free space and in confinement), the validity of the ABP modeling implemented in MD simulations is confirmed. Possible reasons for the small deviation between the two diffusion coefficients are also discussed.