[CP2K-user] [CP2K:21535] Re: Adding capping hydrogens for unstable oxygens in QM/MM simulation - Virtual Site approach?

[Marcella Iannuzzi]

Hello Ben, 

CP2K implements three methods to link the QM and MM parts. See the LINK 
section.
You can find some examples among the regtests, for instance 

QS/regtest-3/C4H10-qmmm-gauss-7.inp

The element used to cap the bond can be changed by setting QM_KIND; the 
default option is hydrogen H.


Regards

Marcella

On Thursday, June 12, 2025 at 10:06:40 AM UTC+2 bensi... at gmail.com wrote:

> Dear CP2K Community,
>
> I'm running QM/MM simulations where several oxygen atoms (some inside and 
> some outside of my QM region) are exhibiting instability. I'd like to 
> stabilize these oxygens by adding capping hydrogens "on the fly" without 
> modifying my original structure files. 
>
> Based on my reading of the documentation, the VIRTUAL_SITE functionality 
> might be applicable, but I'm uncertain about the correct implementation. My 
> specific questions are:
>
>    1. 
>    
>    Is it possible to use VIRTUAL_SITE to add capping hydrogens to 
>    stabilize dangling oxygens in the QM region?
>    2. 
>    
>    If so, what is the correct syntax? I've attempted to understand the 
>    documentation but remain unclear on:
>    - How to properly define the position of the virtual hydrogen relative 
>       to the oxygen
>       - How to include this virtual site in the QM region
>       - How to set appropriate restraints to maintain proper O-H geometry
>       - Whether to not I have to modify the Coordinate and forcefields
>    3. 
>    
>    Alternatively, is there a better approach in CP2K for addressing 
>    unstable oxygens during a QM/MM simulation?
>    
> For context, I'm using CP2K version 7.1 with a QMMM setup where the QM 
> region is treated with DFTB3 and the MM region with AMBER force fields.
>
> Any guidance or examples would be greatly appreciated.
>
> Thank you,
> Ben
>

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