You will be paying Late Filing fee, which is Rs. 20 each day for each month.
So you need to calculate late filing fee for each month individually.
For example, if you are filing GSTR-3B for month of October today, you will need to pay Rs. 20 for each day after due date. If due date for October month was 20th November you late filing fee will be Rs. 4460 (223*20).
Calculate fee for each month using late filing fee calculator. But instead of 50, calculate by 20. This calculator is for normal return and not nil return.