VMD-L Mailing List

From: Goutham (gouthambs_at_gmail.com)
Date: Fri Sep 25 2009 - 02:10:04 CDT

Hey Axel,
Thanks a lot for all the pointers. I will look into the references you have
suggested.

Best
Goutham

On Thu, Sep 24, 2009 at 7:49 PM, Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

> On Thu, 2009-09-24 at 18:23 -0700, Goutham wrote:
> > 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
>
> please look up what how you (properly) compute IR spectra
> from quantum mechanics. that will help you understand why
> the dipole moment.
>
> > resources that I can read to understand better? Also should I be using
> > the position dcds or the velocity dcds?
>
> if you use the dipole moment, you have to use the position dcd,
> for velocity ACF based spectral densities, you need to use the
> velocity dcd, of course, but then you don't use the charge information.
>
> > 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..
>
> the position based spectra make mosst sense in crystals, or else
> you will see spurious peaks. velocity based spectra will be very
> similar to dipole based spectra, i.e. the peak positions should be
> identical, but the peak heights can be very different. as you don't
> consider that motions that don't change the dipole moment, are not
> IR active. with the dipole moment based spectrum, you get closer,
> but you still don't consider the symmetry of the wavefunction, which
> imposes additional rules about what transitions are allowed and
> what not (you'd have to compute the born effective charges or
> transition moments for that).
>
> i don't recall exactly, but the two main references that have
> helped me a lot when i was a graduate student are the book
> "Theory of Simple Liquids" by Hansen & Macdonald, and the
> review on dielectric properties from simulations by
> Madden and Kivelson from the mid 80s. i don't have my phd thesis
> at hand to look up the exact reference, but you should find
> it through literature search engine easily.
>
> cheers,
> axel.
>
> >
> > Thanks
> >
> >
> > Goutham
> >
> >
> >
> >
> >
> >
> >
> > > 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 :
> > > http://ftp.ks.uiuc.edu/Research/vmd/plugins/signalproc/
> > >
> > > (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 akohlmey_at_gmail.com
> > Institute for Computational Molecular Science
> > College of Science and Technology
> > Temple University, Philadelphia PA, USA.
> >
> >
> >
> --
> Dr. Axel Kohlmeyer akohlmey_at_gmail.com
> Institute for Computational Molecular Science
> College of Science and Technology
> Temple University, Philadelphia PA, USA.
>
>