Here is a checklist to work through when setting up a 'Calculated' natural ventilation model:

1. Switch Natural ventilation Model option to 'Calculated'.
2. If you are not modelling daylight you may want to speed simulations up using 'Lump similar windows on surface' on the Advanced tab of the Model options dialog. This makes a big difference in Natural ventilation simulations because each window also has crack and Large Vertical Opening airflow paths and reducing the number of windows simplifies the airflow network as well as the solar distribution calculations. This is the default setting for new models in v.1.2.
3. Decide whether you want to model infiltration. Make appropriate setting under Airtightness on the Constructions tab. Modelling infiltration can give better accuracy and may be necessary to connect all of the zones into the airflow network. But if you are investigating summer natural ventilation strategies (when windows and vents are often wide open and dominate ventilation effects) you may be able to speed up simulations, without compromising accuracy, by switching off infiltration modelling.
4. Make sure that the 'HVAC + natural ventilation operates with occupancy' model option is not checked (Timing model option Typical workday only)
5. Switch Natural ventilation on (HVAC tab).
6. On the Openings tab under External glazing under the Operation header enter the percentage area of glazing that opens.
7. Likewise for Internal glazing.
8. Set door opening frequency and area.
9. Set vent type, if any. Note that you do not have to check 'Vents fitted' for vents you have drawn manually to operate. The 'Vents fitted' data is used to include default vents in the automatuc facade generation, if the surface has default openings.
10. Set operation schedules to define operation of external/internal windows, vents, doors. Schedule values of 1 mean the window/vent/door can operate, a value of 0 means it cannot.
11. Check for natural ventilation setpoint temperatures below heating setpoint temperatures. If this occurs make sure that operation schedules don't allow natural ventilation operation during the heating season.
12. Set the appropriate natural ventilation setpoint temperature on the Activity tab under 'Environmental Control'. When the air temperature in the zone is above the setpoint the ventilation can operate. Holes have no operation schedule or temperature setpoint control.
13. Check that the Natural ventilation 'modulation according to inside-outside air temperature' settings on the Advanced tab of the Model options are set correctly to avoid cold draughts being introduced.
14. Important: Check hourly air change rate and airflow heat gain/loss simulation output for summer and winter conditions before using monthly and annual results. Hourly results can reveal errors in the model much more easily than daily, monthly or annual data.
15. Look at hourly/sub-hourly airflows through individual windows, vents, holes and doors to ensure that flows are as you expect.
    

See also Is DesignBuilder suitable for modelling natural ventilation?