This study aims to obtain insight into the molecular interactions, which cause differences in the interdigitation propensity and phase behavior of MMG analogs with alternative and native-like lipid acid configurations. Our hypothesis is that the stereochemistry exerts a profound influence on the dynamics and spatial orientation of lipids, which affect the relative free energy of the possible different phases, eventually resulting in a specific phase being preferred. We used atomistic MD simulations to compare these properties between MMG-1 and another MMG analog, MMG-6. Only the lipid acid stereochemistry differs between these two analogs; their molecular structures are otherwise identical. 10 Based on previous work, which highlights the slow kinetics of interdigitation of lamellar bilayers, we concluded that simulating all stages of the self-assembly process from a random distribution of lipids to a fully equilibrated interdigitated membrane was not computationally tractable. Furthermore, the simulations were performed below T m of each MMG analog. Therefore, non-interdigitated and interdigitated starting structures were constructed to investigate the conformations, dynamics, and interactions of the two MMG analogs of interest.