In this study, we used MD simulations of various membrane configurations to investigate how the stereochemistry of the lipid acid moiety affects the molecular shape, dynamics, and interactions of MMG analogs. Our aim was to gain insight into the molecular interactions explaining why MMG-1 has been observed to self-assemble into the interdigitated subgel phase and MMG-6 into the non-interdigitated gel phase in low temperatures. The results revealed differences in tail conformations and fluidity of the MMG lipids in the bilayers. Our findings on tail order parameters indicate that the interdigitation of MMG-1 could result from a change in the balance between entropy and enthalpy. However, further experimental validation is required to confirm these results. The results also support the previously suggested idea of MMG-6 being more prone to form an inverted hexagonal (H II ) phase due to a lipid acid configuration that allows the hydrocarbon chains to occupy a larger effective volume. We see our study as an example of a first step in incorporating the insight obtained by combining MD simulation and ML into the design of lipid-based pharmaceutical formulations.