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Mod:Hunt Research Group/Jan cavities

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using Jan's code to visualise cavities

1.3 VdW iso-surface for ch3oh
  • the code you need is cavity.py
  • this can be found in repESP/scripts directory
  • this code generates van der waals radii (VdW) expansions from the atomic centers??
  • it uses a cube file to extract the coordinates and grid to visualise the surfaces (the values associated with the mesh points are irrelevant)
  • you can open this in gaussview, but VMD will be better
  • in gaussview change the "density" to 1.0 (VdW) or more! say 1.4 VdW