Accurate simulation and control of nanoparticle aggregation in chemical reactors requires that population balance equations be solved by using realistic expressions for aggregation and breakage rate kernels. Obtaining such expressions requires that atomistic simulation approaches that can account for microscopic details of particle collisions be used. In principle, molecular dynamics simulations can provide the needed microscopic information, but because of the separation in length scales between the aggregates and solvent molecules, such simulations are too costly. Brownian dynamics simulations provide an alternative to the molecular dynamics approach for simulation of particle aggregation, but there has been no systematic attempt to validate the Brownian dynamics method for this class of problems. In this work we attempt to develop a better understanding of Brownian dynamics simulations of aggregation by (1) developing convergence criteria, (2) determining criteria for aggregation to occur in BD simulations using dimensionless variables, and (3) directly comparing BD and MD simulation predictions for a model aggregation problem.