Appearing as a computational microscope, MD simulation can ‘zoom in’ to atomic resolution to assess detailed interactions of a membrane protein with its surrounding lipids, which play important roles in the stability and function of such proteins. This study has employed the molecular dynamics (MD) simulations, to determine the effect of added DMPC or DMTAP molecules on the structure of DPPC bilayer, and also to characterize the mutual interactions of TM23-GlyR (The second and third transmembrane domains of glycine receptor), with the pure and mixed lipid bilayers. Structural properties of DPPC bilayer, namely the order of acyl chains and the area per lipid, were affected by cationic DMTAP and zwitterionic DMPC lipids, in completely reverse ways. In the case of the mutual interactions of lipid molecules and TM23-GlyR, the cationic DMTAP lipids showed greater impact on the structural properties of this protein. On the other hand, TM23-GlyR caused clear increase in the lipid chain order, due to the positive hydrophobic mismatch. In total, this study could shed light on the effect of lipid force field, chain length, and the head group charge and size, on the lipid-protein interplay.