Mechanistic insights into ligand dissociation from the SARS-CoV-2 spike glycoprotein
Fig 2
Linoleate (LA) dissociation pathways.
(A) The RMSD of LA relative to the initial equilibrated structure for each successful dissociation simulation. A successful dissociation is defined by a ligand RMSD greater than 30 Å. The simulation time before and after the dashed line indicates the GaMD preparation and production run, respectively. (B) Representative trajectories depicting two distinct dissociation pathways: Path A (green) and Path B (orange). The ligand trajectory is shown by individual beads, representing the center of mass coordinates of LA over the simulation time.