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

[Ivan Gladich]

Hi,

You have two options
1) Use CP2k implementation as Marcella previously posted to you. (I did not know was implemented directly in CP2K. Thanks)
2) Use PLUMED plug-in. Your CP2K should be compiled with the option  --with-plumed=install  
If this is the case, you can provide the plumed.dat with all the functions. (Testing and tuning is necessary also in this case)
In the MOTION section as follow

 &FREE_ENERGY
  &METADYN
   USE_PLUMED .TRUE.
   PLUMED_INPUT_FILE plumed.dat
  &END METADYN
 &END FREE_ENERGY


Which solution is easier? 
Not sure, depends on your problem and system.

Hope it helps
Best
Ivan



> On Jul 24, 2025, at 07:41, bijaya pathak <bijayapathak85 at gmail.com> wrote:
> 
> 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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