QM/MM - Gromacs+CP2K ERROR

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1

(last update version)

Hello all,

I am trying to apply QM/MM with Gromacs+CP2K interface but I have an error… I have Gallium and basic, N,O,H,C atoms. CP2K part is giving error. during energy minimization part. Probably gromacs part has a problem as well… I am sharing with you my input and outputs. I didn’t understand anything from error… Thank u in advance… (P.S. First I used to amber22 for creating forcefield parameters for the gallium with metal center parameter builder (MCPB.py). I converted amber parameters with acpype.py for Gromacs))

Please someone make my day… ıf I can understand it error, I can continue…

I uploaded my files to google driver ıf you give some feedback. I will be so glad.

https://drive.google.com/drive/folders/1hVCWpUa0Cy8aJDCPhFj3tknh7TuzzG16?usp=drive_link

2

Is the someone any idea how can I manage this error ““The LU factorization in dgetrf failed””“”"???

3

Hi Isilay,

Sorry I am completely missed the message…
So “The LU factorization in dgetrf failed” message typically means that your QM system are not correctly put into the QM BOX. If you uses your own CP2K input (and as I see you are doing that). Then you should manually center the QM system inside QM box in the input .gro structure. QM Box not located in the center of the whole MM box, it is located at the left bottom corner starting from the coordinates (0,0,0) into the positive direction. Calculate current geometrical center of your QM system and then you use gmx editconf -translate to shift all atoms such that it would allign with QM Box center. Hope this would help

4

Hi Dmitry,

I am happy, you are still here:)…
I followed your instructions but I am still getting same error. Do I also need to change my top file?

Many thanks…

5

Could you please update input files in the google drive?

6

Hi Isilay,

I have tested your input with CP2K 9.1 and it seem to work well for me. Maybe actually the problem is in the CP2K 2023.1 build which you are using?

Have you tried that GROMACS-CP2K on other systems? Like the examples from summer schools?

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Hi Dmitry,

I updated my driver
https://drive.google.com/drive/folders/1hVCWpUa0Cy8aJDCPhFj3tknh7TuzzG16?usp=sharing

I tested GROMACS-CP2K (CP2K 2023.1) on "nma "system which example from summer school. For nma, it was worked

Thank u!!

8

Hi Dmitry,

You are right. I don’t know why but something is wrong with CP2K 2023.1 (at least which I am using on my account). I test it on CP2K version 8.2, my input is working… Thank u again!!! many thank!!

9

Hi Isilay,

Yes, I have just checked GROMACS with CP2K-2023.1 it works for me as well. So something happend to you CP2K-2023.1 installation…

P.S. good that CP2K 8.2 works for you

Best,
Dmitry

10

Thank you!! Good to know that.

Best wishes

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