Free energy simulations of receptor-binding domain opening in the SARS-CoV-2 spike indicate a barrierless transition with slow conformational motions

This online data set accompanies the manuscript entitled "Free energy simulations of receptor-binding domain opening in the SARS-CoV-2 spike indicate a barrierless transition with slow conformational motions." The dataset is composed of the following files: * pmf0-now.dcd -- pmf63-now.dcd : molecular dynamics trajectory frames in each of the 64 umbrella sampling windows, from which water has been removed to save space * s1am_0-now.pdb -- s1am_63-now.pdb : initial coordinates in each of the 64 umbrella sampling windows, from which water has been removed, corresponding to the trajectory data above * view -- Visual Molecular Dynamics command script to load a trajectory, e.g., in Linux, use "vmd -e view" * s1am_0-cg.dcd -- s1am_63-cg.dcd : molecular dynamics trajectory frames in each of the 64 umbrella sampling windows, coarse-grained to 1 bead per residue. * s1am_0-cg.pdb -- s1am_63-cg.pdb : initial coordinates in each of the 64 umbrella sampling windows, corresponding to the coarse-grained trajectory data above. * viewcg -- Visual Molecular Dynamics command script to load a coarse-grained trajectory, e.g., in Linux, use "vmd -e viewcg" * 0readme -- brief instructions on how to view the trajectories * colors.vmd -- utility script for VMD * covmacros.vmd -- VMD script to define coronavirus spike subdomains * fe.zip -- ZIP archive that contains data and Matlab analysis files to reproduce the free energy profiles * diff.zip -- ZIP archive that contains data and Matlab analysis files to reproduce the diffusion and mean first passage times calculations * pca-qha.zip -- ZIP archive that contains the data and Matlab analysis files to compute the autocorrelation functions of trajectory displacements along principal/quasiharmonic modes Each ZIP archive contains a "0readme" file with brief instructions, and also the results of the calculations