This release has additional scripts added for the simulations and analysis described in: MW Grunst, Z Qin, E Dodero-Rojas, S Ding, J Prévost, Y Chen, Y Hu, M Pazgier, S Wu, X Xie, A Finzi, JN Onuchic, PC Whitford, W Mothes, W Li. Structure and inhibition of SARS-CoV-2 spike refolding in membranes. Science, 385, 757–765 (2024). DOI: 10.1126/science.adn5658.