The pervaporation separation of liquid mixtures of water/ethanol and water/methanol using three zeolite (Silicalite, NaA and Chabazite) membranes has been examined using the method of molecular dynamics. The main goal of this study was to identify the role of intermolecular interactions between water, methanol, ethanol and the membrane surface that played a critical role in the separations. This would then allow better membranes to be designed more efficiently and systematically than the trial and error procedures often being used. Our simulations correctly exhibited all the qualitative experimental observations for these systems including the hydrophobic or hydrophilic behavior of zeolite membranes. The simulations showed that for Silicalite zeolite, the separation is strongly influenced by the selective adsorption of ethanol. The separation factor as a consequence increases almost exponentially as the ethanol composition decreases. For ethanol dehydration in NaA and Chabazite, pore size was found to play a very important role in the separation; very high separation factors were therefore possible. Simulations were also used to investigate the effect of pore structure, feed compositions and operating conditions on the pervaporation efficiency. Finally, our simulations also demonstrated that molecular simulations could serve as a useful screening tool to determine the suitability of a membrane for potential pervaporation separation applications. Simulations can cost only a small fraction of an experiment, and can therefore be used to design experiments most likely to be successful.