We aligned two fundamentally different models of smallpox transmission after a bioterrorist attack: A location-explicit multi-agent model (BioWar) and the conventional epidemiological box model, called a SIR model for Susceptible-Infected-Recovered. The purpose of this alignment is part of a greater validation process for BioWar. From this study we were able to contribute to the overall validation of the complex agent based model, showing that, at the minimum, the epidemiological curves produced by the two types of model were approximately equivalent, both in overall and the time course of infection and mortality. Subtle differences on the model results revealed the impact of heterogeneous mixing in the spread of smallpox. Based on this foundation, we will be able to further investigate the policy responses against the outbreaks of contagious diseases by changing heterogeneous properties of agents, which cannot be simulated in a SIR model.