Energy minimization and molecular dynamics simulation are used to develop atomistic models of HCl- and HBr- doped conducting polyaniline, in order to study diffusion and adsorption of water vapor in these polymers. Various morphological properties of the polymers are computed, including their pair correlation functions that are found to be in good agreement with the experimental data, and their accessible free volumes. The sorption isotherms and self diffusivity of water vapor in these polymers are also computed at various temperatures. The computed sorption isotherms are in good quantitative agreement with the experimental data, while the diffusivities are within an order of magnitude of the data. The computed activation energy compares well with that published in literature for water sorption in doped polyaniline.