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Mod:Hunt Research Group/electrostatic potentials 2

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Visualizing Electrostatic Potentials using Molden

1. Generate formatted checkpoint file (either using formchk or adding the formcheck keyword to your input file)

2. Create cube files for the density and electrostatic potential using cubegen:

       cubegen 0 density  jobname.fchk jobname_dens.cube 80  
       cubegen 0 potential jobname.fchk jobname_esp.cube 80

3. Start Molden:

  - Click "Dens.Mode"
  - Click "Read Cube"
  - Select "Gaussian"
  - Enter filename of density cube: jobname_dens.cube
  - Click "Vr" icon
  - Select "Colour Mapped"
  - Select "Gaussian Cube" under "Select Types" 
  - Enter filename of electrostatic potential cube: jobname_esp.cube
  - Select output "VRML2.0"
  - Play around with contour value for isodensity surface
  - Click Apply

4. Visualize .wrl file using software such as "Chimera" (http://www.cgl.ucsf.edu/chimera/)