The protocol allows for scaling the size of the cargo and the LNP and also adapt the core to other LNP structures and shapes. Factors such as the protonation level of the ILs, the N/P (nitrogen to phosphate) ratio, core hydration level, and ion concentration can be customized by the user, guided by existing experimental data. Additionally, PEGylated lipids can be incorporated into the LNP coating as observed experimentally . The protocol utilizes several tools, including TS2CG , Polyply , Packmol , Blender , MDVWhole ,