Development of more efficient solvent solutions for removal of CO2 from natural gas and flue gases is a major task, which contributes to improved design of process plants and leads to decreased costs for its removal. Understanding the mechanisms of CO2 absorption as well as analysis of undesired simultaneous processes is crucially important in this regard. In this work, we have applied Molecular Dynamics (MD) to investigate the absorption of CO2 from a binary mixture of CO2 and CH4 into aqueous piperazine activated MDEA solution. The MD simulations were performed at a constant temperature of 298 K for five different systems with a loading factor of 0.07 to provide insight into molecular distribution in the amine solution and to enhance understanding of absorption mechanisms on the molecular scale. Force field parameters that were missing from the OPLS-AA force field, as well as charge distribution of piperazine (PZ), protonated piperazine (PZH+), piperazine carbamate (PZCOO−) and MDEA were obtained by QM calculations. The results of our simulations emphasize the importance of piperazine and piperazine carbamate in accelerating the absorption process. For the first time, we have shown the undesirable trapping of CH4 by the amine solution and revealed that amine groups are mainly responsible for both absorption of CO2 and the undesired trapping of CH4.