Plotting electron density and orbitals with VMD

[fgygi]

VMD can be used to plot the electronic density from a "cube" file generated e.g. with the plot -density rho.cube Qbox command.
Invoke vmd with the "-e" option as follows:

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$ vmd -e density.vmd rho.cube

where the file `density.vmd` contains the following:

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display projection orthographic
# set background color
color Display Background blue2
#display backgroundgradient on
#color Display BackgroundTop white
#color Display BackgroundBot cyan
#axes location off
mol delrep 0 top
mol representation CPK 0.7 0.2 23.0 21.0
mol color Element
mol selection {all}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol representation Isosurface  0.100000 0.000000 0.000000 0.000000
#mol color ColorID 0
mol modstyle 2 0 Isosurface  0.100000 0.000000 2.000000 0.000000 1 1
mol selection {all}
mol material Opaque
mol addrep top

Note that the origin of coordinates in Qbox is located at the center of the domain represented in the cube file (i.e. an atom positioned at (0,0,0) will appear at the center of the domain).

VMD can also be used to plot orbitals from a cube file generated e.g. using the plot -wf 5 orbital5.cube Qbox command. In that case, the cube file contains two functions: one representing the positive isosurface and one representing the negative isosurface. VMD plots the positive isosurface in red and the negative isosurface in blue. VMD can be invoked as follows:

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$ vmd -e orbital.vmd orbital5.cube

where the file "orbital.vmd" contains the following commands:

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display projection orthographic
# set background color
color Display Background blue2
#display backgroundgradient on
#color Display BackgroundTop white
#color Display BackgroundBot cyan
#axes location off
mol delrep 0 top
mol representation CPK 0.7 0.2 23.0 21.0
mol color Element
mol selection {all}
mol material Opaque
mol addrep top
mol selupdate 0 top 0
mol colupdate 0 top 0
mol scaleminmax top 0 0.000000 0.000000
mol smoothrep top 0 0
mol drawframes top 0 {now}
mol representation Isosurface -0.200000 0.000000 0.000000 0.000000
mol color ColorID 0
mol selection {all}
#mol material Transparent
mol material Opaque
mol addrep top
mol selupdate 1 top 0
mol colupdate 1 top 0
mol scaleminmax top 1 0.000000 0.000000
mol smoothrep top 1 0
mol drawframes top 1 {now}
mol representation Isosurface 0.200000 0.000000 0.000000 0.000000
mol color ColorID 1
mol selection {all}
mol material Opaque

Note that the values of the isosurface are set arbitrarily in the "orbital.vmd" file to -0.2 and 0.2. You may have to adjust the isosurface levels using the Graphics->Representations menu in the VMD main window.
Note that the Qbox plot command can only generate density and orbital isosurface when only the gamma point (k=0) is used.