VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 09 2020 - 17:23:13 CDT

On Tue, Jun 9, 2020 at 6:18 PM MD Simulation <mdsimulationgroup_at_gmail.com>
wrote:

> Hello,
>
> Using the IR Spectral Density Calculator Plugin you can calculate the
> vibrational spectra of an MD trajectory. Does anyone know how to select a
> frequency and then visualize the vibration? Maybe some kind of inverse
> Fourier transform?
>

no. this just computes spectral densities form "vectors" (e.g. velocities,
dipoles, positions) directly over a trajectory. this is not a normal mode
computation.
it is essentially like computing an auto-correlation function and then
doing the fourier transform, but does this in one step and without having
to arbitrarily cut off the unconverged part of the ACF.

axel.

>
> Thanks,
> Chris
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.