[CP2K-user] [CP2K:21548] Re: Adding capping hydrogens for unstable oxygens in QM/MM simulation - Virtual Site approach?

Marcella Iannuzzi marci.akira at gmail.com
Mon Jun 16 11:47:39 UTC 2025


Hi Ben, 

No the LINK methods are restricted to the QM-MM interface.
For an example of use of the VIRTUAL_SITE you can look in the tests 

tests/Fist/regtest-5/water_tip4p.inp

It seems to be specific for FF.



Regards

Marcella



On Thursday, June 12, 2025 at 4:35:18 PM UTC+2 bensi... at gmail.com wrote:

> Dear Marcella,
>
> Thank you for your helpful response. I apologize for not being clearer 
> about my specific situation.
>
> The unstable oxygen atoms I'm dealing with are not actually at the QM/MM 
> boundary - they are fully within the QM region. For example, I have oxygen 
> atoms that are already defined as QM atoms, and all atoms connected to them 
> are also treated with QM. Since these oxygens are not connected to any MM 
> atoms, I don't believe I can use the LINK approach as there is no QM-MM 
> bond to cap.
>
> My understanding is that the LINK section in CP2K is specifically designed 
> to handle bonds that cross the QM/MM boundary, where one atom is in the QM 
> region and the connected atom is in the MM region. Please correct me if 
> this understanding is incorrect.
>
> What I'm looking for is a way to add capping hydrogens to unstable oxygens 
> that are completely within the QM region - essentially adding hydrogens 
> that don't exist in my original structure. Would the LINK approach still 
> work for this scenario, or is there another approach in CP2K more suitable 
> for adding atoms to the QM region during a simulation?
>
> Thank you again for your assistance.
>
> Best regards,
> Ben
>
> Marcella Iannuzzi 在 2025年6月12日 星期四下午6:50:09 [UTC+8] 的信中寫道:
>
>> 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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