Monday, December 21, 2009

Electrostatic potential maps

Figure 3.4. (a) Contour plot of the electrostatic potential of H2O. The maximum and minimum contour value is 0.5 Hartrees/electronic charge (au). (b) The corresponding 0.05 au isopotential surface. (c) The electrostatic potential displayed on the 0.002 au isodensity surface of water. The maximum (darkest blue) value corresponds to 0.05 au.
From Molecular Modeling Basics CRC Press, May 2010.

Here is a screencast of how I made the figure:

The files I used were created in a previous post. The various values specified above are determined using trial and error, i.e. I kept fiddling with it until it looked good to me. When using plots like this it is important to specify these values, because using different values can lead to very different looking plots.

Also, different programs use different color scales and color intensity to indicate positive and negative charge, so it is rarely possible to directly compare electrostatic potential maps from different programs.

See this post about using screen capture to get a file with the graphic. This was done for each plot, and the combined in a word processor.

The interactive version of this figure is the subject of a future post.


polaritythread said...

Looking forward to your book! Working on an intriguing cover?

Jan Jensen said...

CRC Press is, I hope, working on an intriguing cover. In fact, Figure 3.2.2 is supposed to be on the cover somewhere.

Unknown said...

Dear Jan,

Could you explain how macmolplt is able to plot electrostatic potential just by using a .log file from geometry optimization (that does not have any info about the potential, i guess)?

I have found a $ELPOT group along with the GRID keyword in the gamess manual for the electrostatic potential calculation. After trying it i got ELECTROSTATIC POTENTIAL info point by point in my .log file.

Now i am confused what electrostatic potential should i plot: by using a.log file from geometry optimization or by using a .log file from $ELPOT calculation.

I would be grateful to you if you could provide an explanation.