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

[Ben siu]

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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