LNP-endosome stalk system: unbiased MD with 50% deprotonated MC3

All-atom (CHARMM36) system of a HER2-siRNA lipid nanoparticle fused through a stalk with an endosomal-like membrane (MC3, DSPC, cholesterol, PC/PE/PI/SM lipids) in water with 100 mM KCl, in which half of the ionizable MC3 lipids are neutral (148 protonated MC3H, 150 neutral MC3). Unbiased MD to study siRNA translocation/release (Figure 4 and Fig. S17 of the paper). Trajectory without solvent.

Program

GROMACS