[CP2K-user] [CP2K:18627] normal mode analysis on an ab initio trajectory

[Lucas Lodeiro]

Hi Emma,

I do not know how you managed to obtain the IR spectrum from your
trajectory, but I suggest the TRAVIS program to do it:
http://www.travis-analyzer.de/
There is many ways to accomplish it, and the results are very good. Also,
there is the possibility to obtain the "normal modes" of the trajectory
which are consistent with the trajectory IR/Power spectrum.
There are some tutorials, and the program is self explaining:
https://brehm-research.de/spectroscopy.php

In the normal modes section you can feed the program with one or more
minimum energy conformer where the trajectory is projected, and
approximated normal modes are obtained.

Regards - Lucas

El jue, 6 abr 2023 a las 14:21, Emma Rossi (<emma.rossi.1 at studenti.unipd.it>)
escribió:

> Dear all,
>
> I would need to assign the bands of an IR spectrum, obtained through AIMD
> simulation.
>
> I would like to perform a normal mode analysis (NMA) on the trajectory I
> have already produced to properly take into account solvation effects as
> well as the correct weight of the sampled conformers.
>
> I guess I could do so retracing the traj.xyz and using the vibrational
> analysis section in the input, but I would be very greatful if you could
> clarify a few issues about this strategy:
>
> 1) is it the most efficient and correct way to do NMA over a trajectory or
> do you suggest any other ways?
>
> 2) how the output with eigenfrequencies and eigenvectors should look like?
> I can figure the typical output for NMA on single configurations, but I
> have no ideas of what should I expect for NMA on trajectories (I suppose
> that the hessian will be diagonalized at each step, but how these info will
> be put together at the end of the process? )
>
> I have read the original paper of CP2K and the pdf presentations available
> online, but I couldn't fix my problem.
>
> I am very willing to understand and learn from anyone who will help.
>
> Thank you very much in advance for your support.
>
> Best regards,
> Emma Rossi
>
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