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If you are modeling single family or low-rise residential the DOE prototype measure won't have an appropriate building type for you. I would recommend using either BEopt or HPXML directly to generate residential models. The downside for multifamily is that those models are living unit-based and do not include common areas. But from the sounds of your study I don't think that would be a major setback. You would also be limited to unitzed systems (in unit heat pump or furnace for example). but unless you planned to leverage the HVAC system for thermal storage directly that is probably OK. BEopt has a lot of functionality built in, but if you really need additional OpenStudio capabilities you can carry the model into OpenStudio (App or CLI).