Structure files and MD simulation trajectories were visualized and analyzed using Pythonenabled VMD 1.9.4a58. VMD provides a python interface to utilize numpy numerical library and plotting tools like matplotlib. To study the structural difference of the membrane in cis and trans conformation, membrane structure measurements like membrane thickness, area per lipid, membrane diffusion, and membrane order parameters were calculated from the MD trajectory. The membrane thickness was calculated as the distance between the phosphate groups of the two leaflets, and the volume was determined by multiplying the X and Y dimensions of the simulation box by the membrane thickness. Relative z distribution of double bonds and phosphate atoms was calculated using the mean position of phosphate atoms to define the central plane. Area per lipid for individual residues is calculated by finding the distribution of each residue at z [-18,18] and finding the nearest residue on a grid of points to assign fractions of the overall membrane area. The gridding and nearest neighbor determination was accelerated using the SciPy library. Membrane order parameter was determined using the MEMBPLUGIN for VMD. Order parameter is calculated using the equation: