VMD-L Mailing List

From: Jay Shore (Jay.Shore_at_SDSTATE.EDU)
Date: Sun Oct 07 2007 - 15:50:40 CDT

Howdy,

I am creating movies using VMD to incorporate into my General Chemistry and
physical chemistry lectures. I want to show the students electron density
surfaces colored according to the electrostatic potential, but I am not sure
what is the most appropriate Isovalue to choose for the surface. It would be
nice to know what percent of the electron density was encompassed by a
surface. To do this I think that I would have to write a program to
integrate the volume inside the surfaces.

So, my questions:

Am I missing an application that already exists that will convert my cube
files into something resembling percent of electron density? I have done a
lot of searching (googling) but to no avail.

If I do convert the value of the cube file to percent electron density
contained (by integrating the volume of the surface) can I still use VMD to
draw the surfaces. I don't see why not, but maybe I am missing something.

What is the most meaningful way of representing an electron density surface?
Percent electron density contained or the atoms in molecules approach (e.g.
Bader). I know that it depends on exactly what I want to show, but is one
method preferred over another?

If I decide to write the code to do the integration and conversion, is there
a good starting point? I assume that I should do it in C or Fortran because
of the size of the cube files and a script would take too long.

I would appreciate any comments or suggestions.
Thanks,
Jay 

-- 
Jay Shore
Associate Professor
Department of Chemistry and Biochemistry
South Dakota State University
Brookings SD, 57007
phone: (605) 688-6356
fax: (605) 688-6364