VMD-L Mailing List

From: Ignacio Fernández Galván (jellby_at_yahoo.com)
Date: Fri Jun 13 2008 - 05:40:17 CDT

Hi all,

I'm analyzing the solvent structure in some dynamics run, and I find the visual information that can be obtained with volume maps very useful. In particular, I'm using the occupancy volmap (without the -points option in the volmap command) and, while I understand how it is calculated, I would like to know whether it is possible to extract any other, more quantitative, information from the generated .dx file. I would be interested, for instance, in obtaining the number of solvent molecules, in average, in a certain region (delimited by an isosurface).

I guess that I could, for a start, filter the cells in the .dx file with a value larger that the threshold, multiply their value by the cell volume and divide by the volume of the "balls" used to obtain the volmap. Has anyone done anything similar? Any other advice?

Thanks
Ignacio

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