VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Aug 04 2011 - 13:49:06 CDT

On Thu, Aug 4, 2011 at 4:25 AM, Kukol, Andreas <a.kukol_at_herts.ac.uk> wrote:
> Hello,
>
> How can I calculate the IR spectral density by averaging over INDIVIDUAL molecules?
>
> The description of the IR spectral density calculator plugin says:
>
> "Please note that this is using the total dipole moment of all atoms in the selection and not averaging over individual molecules. The latter and other types of auto-correlations can be computed through the script interface of the specden command which is part of the SignalProc plugin collection and described in the respective documentation"
>
> However, after reading the specden documentation, I am not sure how to to average the dipole moment over INDIVIDUAL molecules. Any help would be appreciated.

just have a closer look at the documentation. toward the bottom of the page
there are two examples highlighting the use of the specden command. i suggest
you use the second one as a template, but rather than using lists of positions,
you need to compile lists of the molecular dipole moments (using a list of per
fragment selections and measure dipole) and then process and combine the
individual spectral densities in the same way.

http://www.ks.uiuc.edu/Research/vmd/plugins/signalproc/

cheers,
     axel.
>
> Many thanks
> Andreas
>
>
>
> 

-- 
Dr. Axel Kohlmeyer
akohlmey_at_gmail.com  http://goo.gl/1wk0
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.