[CP2K-user] [CP2K:18631] normal mode analysis on an ab initio trajectory

[Emma Rossi]

Dear Giacomo,

thank you very much for your prompt reply and for your suggestion. 

I think that the strategy you are prosposing is useful for sure to have an 
idea about the contribution of the different bond vibrations to the normal 
modes of a specific conformer. However, I have still doubts concerning how 
to weight the NMA of the different conformers in order to interpret the 
whole IR spectrum. 

In particular, this would be important in case different conformers have 
different normal modes. I think that VDOS analysis could be useful as 
additional check, but information about the weights would be still missing

However, I will try with your strategy and in the meanwhile I'll think 
about the next step.
Thank you very much for the stimulating discussion.

Best regards,
Emma Rossi
Il giorno giovedì 6 aprile 2023 alle 19:29:35 UTC+2 Giacomo Melani ha 
scritto:

> Dear Emma,
>
> You can certainly do a vibrational analysis through the standard input for 
> such calculation (
> https://manual.cp2k.org/cp2k-2023_1-branch/CP2K_INPUT/VIBRATIONAL_ANALYSIS.html). 
> That will read your selected configuration and perform a diagonalization of 
> the Hessian matrix to extract the corresponding normal mode frequencies and 
> eigenvectors. This type of calculation will read a specific geometry. It 
> can also provide you additional information, like IR/Raman intensities, but 
> that requires the calculation of transition dipole moments and 
> polarizabilities.
>
> However, if you already have an AIMD trajectory, you might also want to do 
> a vibrational analysis by computing a time correlation function. For 
> instance, you can extract a vibrational density of states by calculating 
> the time-autocorrelation function of nuclear velocities. For sure, the 
> combination of NMA and correlation functions will give you the best 
> assessment of vibrational modes in your system.
>
> I hope this helps.
>
> Best,
>
> Giacomo Melani
>
> Il giorno gio 6 apr 2023 alle ore 12:21 Emma Rossi <
> emma.r... at studenti.unipd.it> ha scritto:
>
>> 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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