Re: Calculation of IR spectra using VMD IRspec Plug-in

From: Axel Kohlmeyer (
Date: Sun Feb 20 2011 - 12:40:41 CST

On Thu, Feb 17, 2011 at 2:22 AM, Mikhail Suyetin <> wrote:
> Dear Users,


please post VMD questions to the VMD mailing list. that is what it is
for. thanks.

>  I've got a question how to calculate IR spectra of carbon nanotube
> using VMD IRspec Plug-in. It needs charges to form dipole, but C atoms
> in nanotube have no charges.

first of all, you should think for a little bit about what level of realism
you can expect from a classical trajectory. typically people are only
interested in the properties of the non-nanotube objects, and then the
description of a bunch of condensed and rolled up benzene rings is
a good approximation. that lack of polarization - even though a nanotube
is significantly polarizable - also affects the lack of having a (temporary)
dipole moment.

that being said, you can still calculate vibrational frequencies, e.g. by
using velocities or even positions of the individual atoms instead of
the total dipole as input. that will have a significant impact on the
(relative) intensities, but the frequencies are the same. that requires
some tcl scripting and you can see an example for that at:


> Sincerely yours,
> Mikhail Suyetin

Dr. Axel Kohlmeyer
Institute for Computational Molecular Science
Temple University, Philadelphia PA, USA.

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