VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Tue Jun 09 2020 - 18:08:29 CDT

to visualize it, you first need to compute the eigenvectors and those
require the construction and diagonalization of a hessian matrix or
something equivalent like a principal component analysis (which is more
suitable for low frequency collective modes of large objects).

the kind of thing you are looking for is more commonly available as
visualization/post-processing of quantum chemistry codes. this has very
little common what the spectral density plugin does. those spectra are
computed by taking the individual eigenvalues and then applying some
smoothing and estimates of peak intensities from the transition moments.
that is a whole different ball of wax.

axel.

On Tue, Jun 9, 2020 at 6:47 PM MD Simulation <mdsimulationgroup_at_gmail.com>
wrote:

> 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.
>>
> 

-- 
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.