VMD: Render High Resolution Image of Isodensity Surface with Electrostatic Potential

       This post describes how to visualize the electrostatic potential on the total density of molecules in Gaussview. You can do that in the Visual Molecular Dynamics (VMD) as well. Moreover, VMD can render the high resolution of graphics rather than Gaussview using either its built-in renderer or an external renderer like Tachyon graphic.

Displaying Electrostatic Potential.

1. Prepare the density and ESP cube files using formchk and cubegen (Gaussian utility) --> Read this.

2. Read the density cube as a new molecule in VMD.

3. Read the ESP cube as data for an existing molecule.

4. Change the display to Orthographic.

5. Change the drawing method to Licorice in Graphics/Representations.

6. Create a new representation with a drawing method of Isosurface.

7. Change Draw to Solid Surface.

8. Change Show to Isosurface.

9. Adjust the isovalue to 0.04 (recommended value).

10. Change the Isosurface coloring method to Volume, selecting the ESP cube in the adjacent box.

11. Adjust the color data range under the Trajectory tab.

12. Add the color scale bar through the Extensions menu.

13. Use the internal Tachyon graphic renderer. 

14. Then set the Selected Atoms to element.

Optional: You can highlight a particular atom by adding a new representation and setting the Drawing Method to VDW.

Recommended setting for rendering high-resolution images.

• Colors: An RWB color scale with a midpoint of 0.50 to 0.65.Material Settings:

• Ambient = 0.30

• Diffuse = 0.43

• Specular = 0.25

• Shininess = 0.65

• Opacity = 0.69

• Outline = 0.07

Rangsiman Ketkaew