Jono,
It sounds like you're trying to model the behavior of a VAV system in which the supply airflow to each zone is regulated by an indvidual control damper. A damper is closed or opened according to a fixed schedule - for example, the damper admitting supply air to a zone opens at 8 am to allow for cooling or heating, and closes at 8 pm when the building is vacant for the evening. Do I have that correct?
If so, I don't think there is a way to force airflow to individual zones to be on or off at certain times in eQuest (though other modelers, please correct me if I'm wrong on this point). The "minimum flow schedule" you're referring to, which I'm assuming is the Minimum Flow Schedule shown in the Air Flow tab of a zone's dialog box, does just that - sets a minimum value for the supply air flow. If the zone still calls for heating or cooling during a particular hour, then air will still be supplied to the zone even if the Minimum Flow Schedule value for that hour is zero.
Even though I doubt there's a way to schedule supply air flow on or off for individual zones with a VAV system, you can still do so at the system level. You do this with the Fan Schedules input under System -> Fans -> Fan Power and Control. I suggest reading the input's eQuest help page to learn more, but in brief, if you set the value for a particular hour of the schedule to be -1 the supply air fan at the air handling unit won't be allowed to turn on for any reason. Naturally, this will prevent supply air from flowing to any zone. As long as you're fine with all zones being cut off at the same time, I think this is a workable solution. If you really do need some zones to be forced to have no air while others are allowed supply air, you might need to find a more creative workaround. If you have groups of zones which operate on the same schedule, you can put them on a separate air handling unit with its own fan schedule - though you'll have to be careful about apportioning fan power appropriately.
Hope this helps, and good luck!
Drew
