[CP2K-user] [CP2K:21684] Re: Hydronium_distance CV

[Ivan Gladich]

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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