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

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