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Transistors are the most important part in the development of microprocessor systems. However, the size of transistor cannot be reduced again due to its material size limitation. A new type of transistor is needed, namely single electron transistor (SET). This transistor transports electrons one by one through the quantum dot (QD) using the coulomb blockade effect. SET can be used to make low-power quantum computing device. This research simulates the effect of capacitance in double quantum dots single electron transistor (DQD-SET) using SIMON 2.0. There are two configurations of DQD-SET; series and parallel systems. This simulation uses an experimental approach where the current sensor is placed close to the drain. The value of middle capacitance (CM) and tunnel junction capacitance (TJ) of DQD-SET configurations are varied to observe changes in I - V characteristics. As a result, capacitance values of CM and TJ affects to the current rate change i.e., number of peaks and peak value which is associated with the distance of QD. When the value of CM decreases, an additional current appears between the two initial current peaks. This happens due to clustering effect on QD. [ABSTRACT FROM AUTHOR]