VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_cmm.chem.upenn.edu)
Date: Thu Jun 19 2008 - 05:20:24 CDT

On Thu, 19 Jun 2008, Ignacio Fernández Galván wrote:

IFG>
IFG> Thanks for your reply, John. Actually, I'm already doing that: my
IFG> system is a single 20-atom molecule in water (800 molecules), and I
IFG> calculated the occupancy of water oxygen atoms averaged all along a
IFG> trajectory. When I display an isosurface, I can clearly see the
IFG> regions of space around the solute where the solvent molecules are
IFG> more concentrated (where they form H-bonds, mainly). My question
IFG> was whether (and how) I could extract any other information that is
IFG> not of visual nature. For instance, I would be interested in
IFG> integrating the volume inside the isosurface, weighting by
IFG> occupancy, so as to get the average number of oxygen atoms in a
IFG> given region. It would also be interesting to get the coordinates
IFG> of the maxima in the volume data.

ignacio,

what you are describing sounds a lot like what people do
to analyze electron densities when they do a "Bader" analysis.
most tools i know need the gridded data in a "cube" format
file. so you'd have to save the output from your script to
a file and then convert it to a cube file.

as to integrating the grid points to get the number of atoms
in a region, you just have to take the sum over all grid points
and normalize it so the total is the total number of selected
atoms. then you only have to sum up over grid points that you
identify as a region to get the average number of atoms in
that region. the bader analysis codes can do that directly,
since electron density cube files are in general normalized
in a similar way. have a look, e.g., at:
http://theory.cm.utexas.edu/bader/

cheers,
   axel.

IFG>
IFG> Thanks again,
IFG> Ignacio
IFG>
IFG>
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IFG> 

-- 
=======================================================================
Axel Kohlmeyer   akohlmey_at_cmm.chem.upenn.edu   http://www.cmm.upenn.edu
   Center for Molecular Modeling   --   University of Pennsylvania
Department of Chemistry, 231 S.34th Street, Philadelphia, PA 19104-6323
tel: 1-215-898-1582,  fax: 1-215-573-6233,  office-tel: 1-215-898-5425
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If you make something idiot-proof, the universe creates a better idiot.