Author Topic: Visualization vibration modes? aoforce2g98  (Read 272 times)

baishaotao

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Visualization vibration modes? aoforce2g98
« on: May 03, 2020, 09:44:17 pm »
Dear friends,

I have a problem to visualize the vibration modes after aoforce calculations. I have tried 'aoforce2g98 aoforce.out > g98.out' to convert the turbomole output into GAUSSIAN98 formate. It still does not work!

I have copied the example from molden wibsite http://cheminf.cmbi.ru.nl/molden/examples/vibration.gal. This example works well.

Does anyone has an idea or suggestion to fix this problem or other suggestions?

Many thanks in advance!

Best,
Dr. Shaotao Bai
KU Leuven

uwe

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Re: Visualization vibration modes? aoforce2g98
« Reply #1 on: May 03, 2020, 11:28:29 pm »
Hello,

hard to say what the problem is, but to visualize the modes, just run TmoleX and open the control file. In the Results section there is a button 'Vibrations' It opens the 3D builder which can visualize the modes or combination of modes.

TmoleX Client can do that too, that is the free version of the graphical user interface for Turbomole, available for download from here:

https://www.3ds.com/products-services/biovia/products/molecular-modeling-simulation/solvation-chemistry/turbomoler/

Just click on 'TmoleX - the graphical user interface' and you will find the download links.

Regards,

Uwe

baishaotao

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Re: Visualization vibration modes? aoforce2g98
« Reply #2 on: May 07, 2020, 12:00:17 pm »
Hellow uwe,

Thanks for your kind suggestions.

I have looked into this TmoleX. Unfortunately, reading the control file from remote cluster does not work as expected because it cannot link to my aoforce.out and vib_normal_modes etc. I guess that is a missing excuting script, i.e. TmolexX, therefore the jobs performed in linux cluser cannot be read by TmoleX in windows. If you know how to solve this issue, please let me know.

Anyway, thanks again!

Best,
Dr. Shaotao Bai
KU Leuven

uwe

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Re: Visualization vibration modes? aoforce2g98
« Reply #3 on: May 07, 2020, 12:15:22 pm »
Hello,

just copy the whole directory of your calculation from the Linux box to your Windows system. TmoleX does not need to read in the output file, as all results are stored in the control file or files referenced by it (like the vibspectrum file).

Then, in TmoleX, use File -> Open Job/Control File  to read in the control file. Switch to the Results panel. The buttons on the right side (vibrations , IR spectrum, thermochemical properties, etc. should be accessible).

Regards,

Uwe

baishaotao

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Re: Visualization vibration modes? aoforce2g98
« Reply #4 on: May 07, 2020, 12:46:27 pm »
Hello Uwe,

Many thanks. It works now.

Best,
Dr. Shaotao Bai
KU Leuven