[CP2K-user] [CP2K:18632] normal mode analysis on an ab initio trajectory

[Emma Rossi]

Dear Lucas,

Thank you very much for your suggestion. I obtained the IR spectrum through 
the dipole moment of the whole box computed at each step of the trajectory 
by CP2K. Unfortunately, I couldn't use TRAVIS since I had not printed the 
electron density during the simulation.

However, it would be great if I could use TRAVIS as post processing tool to 
perform NMA on the trajectory. As far as I have seen in the documentation,  
the online tutorials/presentations deal only with the simulation of the 
spectra, which, indeed, require electron density. I couldn't find any 
instruction about how to perform the NMA (I've found just the original 
paper). 

However, if you have expertise in TRAVIS usage, I would be very grateful if 
you could answer a doubt about TRAVIS NMA tool.

Can I perform NMA on my trajectory without performing as a preliminary step 
the calculation of the IR spectrum? As I mentioned above, I have not the 
electron density.

Thank you very much for your kind support.

Best regards,
Emma Rossi






Il giorno giovedì 6 aprile 2023 alle 23:59:45 UTC+2 Lucas Lodeiro ha 
scritto:

> 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.r... 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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