A numerical study of the parameters controlling the viscous penalty method is investigated to better set up Particle-Resolved Direct Numerical Simulations (PR-DNS) of particulate flows. Based on this analysis, improvements of the methods are proposed in order to reach an almost second order convergence in space. The viscous penalty method is validated in Stokes regime by simulating a uniform flow past a fixed isolated cylinder. Moreover, it is also utilized in moderate Reynolds number regime for a uniform flow past a square configuration of cylinder and compared in terms of friction factor to the well-known Ergun correlation.