[CP2K-user] [CP2K:15640] Power Spectrum. Help wanted.

z sh zsh1... at gmail.com
Mon Jun 28 22:05:06 UTC 2021

Dear Lucas

Thanks for your helping.

On Sunday, June 27, 2021 at 4:58:04 PM UTC-7 Lucas Lodeiro wrote:

> Hello, 
> Computing a single molecule MD is not easy, and many things have to be 
> checked. Running a single molecule NVT simulation is difficult due to the 
> thermostat not being well behaved. Also it is important to check the 
> angular momentum of the system is practically zero, because the rotational 
> movement could make "fake signals", also the system linear momentum affect 
> the power spectrum at 0 cm⁻¹. There are keywords to control both. If your 
> power spectra shows a non zero value at cm⁻¹, probably you have one or both 
> problems.
> About the signal at 3700cm⁻¹, the high frequency signals needs a time step 
> of 0.5 fs or at least 1.0 fs, also, if you use a short time step, you need 
> to save the coordinates at each step. Also, if you can print the 
> instantaneous velocities from the MD, you can use them directly and not 
> approximate them by differentiation of coordinates, as done by TRAVIS when 
> only the xyz file is used.
> Remember the power spectra shows signals where their area is proportional 
> to the number of modes at each frequency frame. Also, if your system has 
> more than one methanol molecule, maybe there are H-bonds, which weakens the 
> O-H bonds and "moves" those signals to lower frequencies.
> Regards
> El dom, 27 jun 2021 a las 18:31, z sh (<zs... at gmail.com>) escribió:
>> Hello everyone,
>> I am trying to do vibrational analysis for gas phase system. I am 
>> following the tutorial " Computing Bulk Phase Vibrational Spectra with CP2k 
>> and TRAVIS (2018)". Initially i have done massive equilibration of methanol 
>> system for 6000 steps. After that i have done production run for 60000 
>> steps. Then, I calculated the power spectrum with xyz. file. Unfortunately, 
>> O-H stretching vibration at 3700 cm-1 is not seen in the power spectrum. 
>> Would you please guide me why peak 3700 cm-1 is not seen? 
>>  Here i am attaching my power spectrum.
>>  Please help me on this.
>>  Thanks.
>> [image: power.png]
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