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