Beautiful Molecular Orbital Images from Gaussian Output using VMD

Gaussview can make basic MO images but VMD is a great tool for publication-quality images. We will export cube files from GaussView and use them to render images in VMD. This protocol should also work for any other cube file (electron density, etc.).

1. In GaussView, File/Open and read in the checkpoint file containing the molecular orbitals (or NBOs). Open the molecular orbital editor window (click on the icon with the red/green p orbital), which will show the molecule on the left and an MO diagram on the right. Select the orbitals you want to visualize by clicking on the number of each orbital, highlighting it.

Note: GaussView is currently a little buggy, meaning the orbital diagram isn't displayed correctly if you scroll up. The workaround is to grab the bar separating the diagram from the molecule viewer, pull it to the right until you cannot see the diagram, then pull it back.

Select the Visualize tab (in the MO editor window), and click the Update button on the right side of this window. When the graphics generation is complete, click on the small gray box to the right of the MO you want to examine. If your MO lobes appear too large or small, you can adjust the Isovalue and regenerate the surface (a larger positive value makes the lobes smaller).

2. Generating the cube files.

In the main GaussView window, select Surfaces from the Results menu. Select Cube Actions --> New Cube. Enter the orbitals you want (can be multiple, e.g. 90,95,98 or 99-101), specify the Grid size, and click OK.

Note: if you entered multiple orbitals with a Fine grid, it could take a couple of hours to generate the cubes, and the file you save will be multiple gigabytes in size. Don't forget about it!

The job is finished when the Cubes Available field in the Surfaces and Cubes window is non-blank. With the first cube in the list selected (blue), select Cube Actions --> Save Cube, and name the file to be produced. This file will have the suffix .cub and contain all of the cubes you created.

3. Rendering in VMD.

A. Loading files.

Type vmd on the command line to start the program. In the VMD Main window, select File --> New Molecule, which opens the Molecule File Browser. Browse for yourfilename.cub and click OK. Select the orbital you want to render first from the Volumetric Datasets field and click the Load button. It may take a couple of minutes for the file to be read in. When it's finished, you should see your molecule in the Display window, in stick representation.

B. Molecular representation/display format.

In the Display menu, click on Orthographic. Also select Display --> Axes --> Off. You can rotate the molecule by dragging in the Display window with the left mouse button, or select Mouse --> Scale Mode to zoom in and out. Under the Graphics menu, select Display --> Background and select the color you want. Select Graphics --> Representations. In this window, select Drawing Method --> CPK (this specifies a ball and stick representation, you may prefer tubes or lines), then Coloring Method --> Element. You can adjust the size and resolution of spheres and bonds; a value of 30 in both resolution fields should work fine. To change the atom colors, go to the VMD Main window and select Graphics --> Element and then the color for each element.

C. Creating orbital isosurfaces.

In the Graphical Representations window, click on the Create Rep button. This creates a new, identical representation that you can then change. Select Drawing Method --> Isosurface, and Coloring Method --> ColorID. In the Isovalue field, enter the optimal isovalue you determined in GaussView or use the value 0.04 (you can adjust this later) and press Enter (keyboard key). Change the Show pulldown to Isosurface. This procedure only creates the positive phase of the orbital. The negative phase portion must be generated separately according to the following:

Click Create Rep again, creating a third representation. Change the field immediately to the right of Coloring Method to 4 (yellow), and change Isovalue to the negative of the current value (-0.04 here).

Note: it is NEVER correct to use numbers of unequal absolute value for the two phases, even if it would look better that way!

You should now see the whole orbital, in blue and yellow with the surface represented by points. You can toggle between the positive and negative surfaces by selecting from the list of representations (blue part of the Graphical Representations window). Now change the Draw pulldown to Solid Surface for both phases: Here is your beautiful picture! Experiment with other settings in the Draw and Materials pulldowns (you can make the surfaces transparent, glossy, etc.).

D. Saving the picture.

VMD can interface with a variety of rendering software, but the program's snapshot utility should be sufficient for most uses. Select Render from the File menu and name the file yourfilename.tga, then click Start Rendering. Imagemagick will automatically open with your file displayed; you can save it as whatever format you prefer from there, although .jpg or .bmp are probably the most universally compatible picture formats.