Visualizing Molecular Obitals with gOpenMol

The Gaussian Cube files generated by oeprop can be converted and viewed with gOpenMol. gOpenMol offers good looking plots in a graphical user interface. Information on downloading gOpenMol and samples of gOpenMol output may be found at http://www.csc.fi/gopenmol/.

Installation instructions are included with the gOpenMol download. Once installed, the first step to viewing molecular orbitals is to convert the mo.cube into a format that gOpenMol recognizes. Under the Run menu, select gCube2plt/g94cub2pl (cube) $\dots$, this will bring up a window with the heading Run gCube2plt/g94cub2pl. In the input file name field, select the mo.cube file you want to convert. Likewise, in the output file name field type the name of the output file you want. Click the Apply button to perform the conversion. This procedure will create a .plt and a .crd file. Once converted, click Dismiss to close the window. The Gaussian Cube file is now converted and in a form that gOpenMol can recognize.

In order to view the molecular orbital, the first step is to import the coordinate file (.crd). This is done under the File menu$\rightarrow$Import$\rightarrow$Coords$\dots$. Again, a window will pop up. In the Import file name field chose the .crd you just created from the conversion procedure. Click apply, then Dismiss to close the window. Now we have to import the .plt file to view the molecular orbital. Under the the Plot menu selct Contour$\dots$, this will bring up a window. In the File name field, either type the full path of the file name or use browse to select the .plt file you just created in the conversion, then click Import. In the Define contour levels we have to define the contour cutoffs for the positive and negative parts of the wave function seperately. I recommend trying 0.1 in the first box and -0.1 in the second. Click Apply to view the molecular orbital. You can change the colors of the positive and negative sections independently by clicking on the Colour button next to the respective cutoffs. Also, in the Details$\dots$ section, you can fine tune the properties of the molecular orbital, such as, the opacity, solid vs. mesh, smoothness, and cullface state. You can play around with various settings to get the surface to look exactly how you want it to. There is more information in the Help$\rightarrow$Tutorials menu on this subject as well as many other abilities of gOpenMol.