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I would add that you want to be careful how you model your baseline system, you need to have the same outdoor air in both proposed design and baseline case. In the past when we have modelled natural ventilation for LEED we have asked the mechanical designer for the minimum outdoor air that will be in the space from natural ventilation, this is then continuously put into the space through the simple natural ventilation object in energyplus. The conditioning of the space is then done using either what is designed, or if nothing is designed the baseline system with no outdoor air through this system. In the baseline case, the minimum amount of outdoor air is brought through the baseline system and is conditioned to meet the space requirements. In this case it is important to show that your unmet load hours are low in both cases and that the zones are being conditioned correctly.