Running my proposed against my baseline I got very high fan loads... Did I select the right system?

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There are a few things about LEED models and flow rates that you might want to check.

1. When choosing the baseline system, it depends on the fuel being used in the proposed design, floor area and number of storeys. This can all be found in appendix G.
2. the outdoor air flow rates between the proposed design and baseline must be the same (there are a few exceptions but probably not for this case)
3. How to model the fan power in the baseline is clearly laid out in appendix G without much exception.

To check if your models are running as you expect, look at the outputs, are the fans running at night? should they be running at night? is your fan pressure drop much higher in the proposed case than the baseline case? do you have a lot of heating energy use or is your fan providing the majority of the heating? These things will tell you a little bit more about what the model is doing and whether it is doing the right thing. If you are using energyplus, you can report out the flow and temperature before and after the fan which will give you a lot more information about what is happening in the model.

ASHRAE 90.1 System 6 is VAV. If i understood you have 2 speed fans and constant volumen fans. Usually VAV system reduce up to 60% energy consumption in comparison with constant volumen fans.