From: Goutham (
Date: Thu Sep 24 2009 - 20:23:39 CDT

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 guess I pushed reply, instead of "reply all". I did intend to send to the
group ...

    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
> answer.
> Can you tell me what is the physical basis for using dipole moment to
calculate the spectral density? Can you give me any pointers to resources
that I can read to understand better? Also should I be using the position
dcds or the velocity dcds?

One can calculate spectral densities from different quantities, (like dipole
moment, or using velocity of each atom and then averaging the spectral
density over the atoms).. I am trying to understand, how the spectral
densities will change depending on the kind of quantity that we use...
Should they all be similar? Any pointers will be very helpful..



> > 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.
> cheers,
> axel.
> >
> >
> > Thanks
> > Goutham
> >
> >
> >
> >
> >
> --
> Dr. Axel Kohlmeyer
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.