From: Axel Kohlmeyer (
Date: Thu Sep 24 2009 - 09:30:33 CDT

On Wed, 2009-09-23 at 18:51 -0700, Goutham wrote:
> Hey Axel,


please always direct all questions about VMD that do not
concern me personally to the VMD mailing list. this way
other people get a chance to see the question and answer.
please keep in mind that for every person asking a good
question there are at least ten, that don't dare.

> I was wondering if you could clarify a doubt:
> Am I right to understand that, IRspecGUI tool in VMD calculates the
> spectrum from the time series of the total dipole moment.

that is mostly correct. the code computes the dipole moment
of the atoms in the given selection based on the value stored
in their charge property. it uses a classical non-periodic
approach for that, but if you have trajectories wrapped by
residue (and neutral charge groups), it should give the same

> Now if I wanted to calculate the spectrum as a Fourier Transform of
> Velocity auto correlation, then should I use similar to example 2 in :
> (i.e.) find the spectrum for each atom in the system, and then get an
> average over all the atoms.

right, you can take about any property, create a list, and then feed it
to the code and it will produce the spectral densities, _not_ the
spectrum, as the code has no knowledge of the transition moments.

please also note that the implemented algorithm computes the spectral
densities directly in fourier space, i.e. the explicit auto-correlation
will not be computed as an intermediate result. this bypasses a lot
of the arbitrariness and undesirable scaling behavior of computing
auto-correlation functions.


> Thanks
> Goutham


Dr. Axel Kohlmeyer 
Institute for Computational Molecular Science
College of Science and Technology
Temple University, Philadelphia PA, USA.