MDVContainment , the Insane script , and VMD , combined into four steps (detailed in the Methods section). Figure provides an overview of the four main steps involved in the building protocol, along with two test cases demonstrating different possible organizations for larger particles. The protocol and scripts are available on GitHub (Force-Field-Initiative/M3-Ionizable-Lipids/). Since the protocol is based on highly versatile tools such as TS2CG and Polyply , it can be used as a starting point for constructing other LNP structures, such as the 'bleb' compartment LNP see in 5. While Lipid 10 and MC3 maintained an inverse hexagonal phase, Lipid 2 formed a multicompartmental vesicle with lipids preferring a lamellar organization (Figure ). Intermolecular radial distribution function (RDF) between RNA surfaces of MC3 LNP did not evolve significantly during the simulation, with two peaks, at 4.7 and 9.3 nm (Figure ). Lipid 10 was less organized, with RDF peaks at 4.3, 8.4 and 10.7 nm. Visually, both these LNPs preserved the inverse hexagonal phase for at least part of the LNP, in agreement with experimental observation of MC3 . On the other hand, Lipid 2 reshaped its internal organization, formed multicompartmental vesicle with RNA located on the water/lipid interface (Figure Panel A), seemingly similar to the reported 'bleb' compartments observed with Cryo-EM pictures .