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

Lucas Lodeiro eluni... at gmail.com
Sun Jun 27 22:57:30 UTC 2021


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
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.


El dom, 27 jun 2021 a las 18:31, z sh (<zsh1... 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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