We model numerically the process of a thermally activated decay of a metastable state over a low barrier in the overdamped regime. This process is typical for the recent nanoscale experiments reported in the literature. Within the framework of a novel unified computer code, two ways of modeling are applied: (i) the partial differential equation (Smoluchowski equation) and (ii) the stochastic ordinary differential equation (Langevin equation for the generalized coordinate). The advantages and disadvantages of both approaches are discussed and analyzed. Special attention is paid to the transient stage of the process yet the quasistationary stage is considered as well.