[CP2K-user] [CP2K:21685] Re: Hydronium_distance CV

[Marcella Iannuzzi]

Dear Bijaya, 

The hydronium distance is implemented in CP2K, but not very much tested. 
The definition of the parameters is the same as the one in the reference 
paper. 
As for the original example, it needs a lot of testing to find the optimal 
settings and it can become unstable due to the exponential functions. 
Regards
Marcella


On Wednesday, July 23, 2025 at 1:35:01 PM UTC+2 igladi... at gmail.com wrote:

> Dear Bijaya
>
> The hydronium distance defined in  (J. Am. Chem. Soc.,128, 2006, 11318) is 
> not trivial to be implemented in CP2K alone.
> You can give a look to the supporting information of 
>
> https://www.nature.com/articles/s41467-024-53186-5
>
> There, PLUMED plug-in was used to code the CV to be then used in 
> combination with CP2K. 
> You may take inspiration.
> If I recall well, in the supporting information there is also an input 
> example. 
>
> Hope it helps.
> Best
> Ivan
>
> On Monday, July 21, 2025 at 3:00:16 PM UTC+3 bijaya pathak wrote:
>
>> Dear all, 
>> I would like to know the function that's been used to describe the CV 
>> Hydronium_distance  which appears to consider the distance between the 
>> distance between hydroxide ion and hydronium ion. There are lots of 
>> parameters given in the subsection I believe is derived from (J. Am. Chem. 
>> Soc.,128, 2006, 11318).
>> Can anyone help me understand what do these parameters mean ? 
>>
>> Section to define the formation of a hydronium as a collective variable. 
>> Distance between hydronium and hydroxide ion Experimental at this point, 
>> i.e. not proved to be an effective collective variable. [Edit on GitHub 
>> <https://github.com/cp2k/cp2k/blob/master/src/input_cp2k_colvar.F#L1402>]
>> Keywords 
>> <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#keywords> 
>>    
>>    - 
>>    
>>    HYDROGENS 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.HYDROGENS>
>>    - 
>>    
>>    LAMBDA 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.LAMBDA>
>>    - 
>>    
>>    NH 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NH>
>>    - 
>>    
>>    NN 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.NN>
>>    - 
>>    
>>    OXYGENS 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.OXYGENS>
>>    - 
>>    
>>    PF 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PF>
>>    - 
>>    
>>    PM 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.PM>
>>    - 
>>    
>>    POH 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.POH>
>>    - 
>>    
>>    QF 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QF>
>>    - 
>>    
>>    QM 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QM>
>>    - 
>>    
>>    QOH 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.QOH>
>>    - 
>>    
>>    ROH 
>>    <https://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/HYDRONIUM_DISTANCE.html#CP2K_INPUT.FORCE_EVAL.SUBSYS.COLVAR.HYDRONIUM_DISTANCE.ROH>
>>    
>> Greatly appreciate any suggestions
>> Thanks 
>> Bijaya
>>
>

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