VMD-L Mailing List

From: Kukol, Andreas (a.kukol_at_herts.ac.uk)
Date: Thu Aug 04 2011 - 03:25:17 CDT

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.

Many thanks
Andreas