Sunday, December 27, 2009

Electrostatic potential maps reloaded

Here is an interactive version of a figure I described in a previous post. Click on the picture to load it. Remember it's Jmol so you can rotate it and zoom as you like (Mac users: this works best with Safari).
Figure 3.4. The RHF/6-31G(d) electrostatic potential of water.
Click on the picture for an interactive version

The Jmol animation loads a file (, which you can access by right-clicking on the Jmol animation once you have loaded it (as described in a previous post). This file also contains all the necessary commands.

Figure 3.4.c is the most common depiction of electrostatic potential maps and the Jmol general syntax for the command for this is
isosurface 0.002 "density.cube.gz" color range -0.05 0.05 "potential.cube.gz"
The screencast below shows how I made the cube files that contain the electron density and electrostatic potential information using MacMolPlt. The first part is identical to the screencast in a previous post on obtaining the electron density cube file.

The program I used to convert the MacMolPlt file to a cube was written by Jonathan Gutow and can be download here.

I start by loading the RHF/6-31G(d) optimized geometry I computed for a previous post, and reorienting. The orientation makes it easier to define the plotting plane for the contour plots.

1 comment:

esben said...

Thank you for a wonderful and useful blog. Am I correct that the command should be:

isosurface cutoff 0.002 "density.cube.gz" color range -0.05 0.05 "potential.cube.gz"

or am I missing something (it could well be, I'm not very experience with jmol, but this way I could make it work)