Steered MD pulling of siRNA from the LNP through the endosomal stalk

All-atom steered MD in which the HER2 siRNA is pulled away from the LNP lipids, through the LNP-endosomal membrane stalk, to transfect it. The pull is an umbrella-type moving restraint along Y (rate 0.0003 nm/ps, k 1000 kJ/mol/nm^2). The frames were used to set up the umbrella sampling windows. Data related to the manuscript 'When lipids embrace RNA: pH-driven dynamics and mechanisms of LNP-mediated siRNA delivery' (Fig. 4).

Program

GROMACS 2023.3