When generating the simulation box, four pairs of disulfide bonds were added according to Uniprot entry P0DTC2 SPIKE SARS2 [7]. They are between residues (4, 29), (47, 100), (59, 193), and (148, 156). With inappropriately generated initial structures, the simulation trajectory can be far away from the experimental structure. They likely still represent some free energy local minima, but are not relevant to the structure features explored in the long MD. The long MD starts with the same initial structure but different initial velocity. It's likely to explore all the regions close to the reduced MSA structures.