VMD-L Mailing List

From: MD Simulation (mdsimulationgroup_at_gmail.com)
Date: Tue Jun 09 2020 - 17:47:15 CDT

Hi Axel,

Thanks for the reply

Sorry for not being clear. What I'm wondering is if there is a method to
visualize vibrations of a specific frequency? For instance, if we have a
molecule with a calculated vibration at 1650 cm^-1, is there a signal
processing method to isolate and visualize that vibrational trajectory?

Thanks,
Chris

On Tue, Jun 9, 2020, 6:23 PM Axel Kohlmeyer <akohlmey_at_gmail.com> wrote:

>
>
> 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.
>