VMD-L Mailing List

From: Ignacio Fernández Galván (jellby_at_yahoo.com)
Date: Thu Jun 19 2008 - 02:43:11 CDT

--- On Thu, 19/6/08, John Stone <johns_at_ks.uiuc.edu> wrote:

> You can use atom selections when computing maps with
> volmap, thereby
> controlling exactly what atom types are contributing to the
> occupancy
> density values in space. By selecting just your solvent
> atoms, you
> can compute a density map of just that property. You can
> then render
> multiple overlapping isosurfaces of the various properties
> you're
> interested in seeing.

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

Thanks again,
Ignacio

      __________________________________________________________
Sent from Yahoo! Mail.
A Smarter Email http://uk.docs.yahoo.com/nowyoucan.html