The Minimum Fee entered is for the full year.   If you run fees quarterly, and the calculated admin fee amount for the quarter is less than 1/4th of the minimum, then it will apply 1/4th of the minimum for that quarter.   If the calculated admin fee amount for the quarter is more than 1/4th of the minimum, then the calculated admin fee amount for the quarter will be used.  

The Annual Minimum Fee is charged upfront and then the system uses your Asset Based fee configuration to determine the ongoing fees. Once the fees exceed the annual minimum, additional fees will be charged based on the rates you set up.