Editing VMD (section)

== Create MO plots with VMD & Gaussian ==

'''!!You need the formatted .fchk from Gaussian!!'''

To get it go to [[Cesca]], and [[G09]] for the tips on how to convert the .chk file in .fchk file.

Once the .fchk is done follow this process: 
  
Gaussian includes a standalone utility for generating cubs from the data in a formatted checkpoint file.[[http://www.gaussian.com/g_ur/u_cubegen.htm]].The utility is named cubegen, and it has the following syntax:
          
          cubegen 0 MO=n  file.fchk  file.cube 0 h

MO=n: Molecular orbital n. 
The keywords Homo, Lumo, All, OccA (all alpha occupied), OccB (all beta occupied), Valence (all valence orbitals) and Virtuals (all virtual orbitals) may also be used in place of a specific orbital number. There is no default for n, and an error will occur if it is omitted.

Then you can open the file with VMD and first get the geometry of your molecule. In a second step an isosurface with the positive and negative values of the electronic wavefunction or with the density can be added.