[CP2K-user] [CP2K:21687] Re: Hydronium_distance CV

[bijaya pathak]

Dear Ivan, 
Thank you so much for your reply. It does help.
To clarify what you said, If I use the plumed plug-in with cp2k, it should 
work if I define my functions in plumed.dat and supply it to cp2k ? 
Thanks and regards
Bijaya

On Wednesday, July 23, 2025 at 5:05:01 PM UTC+5:30 Ivan Gladich 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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