[CP2K-user] [CP2K:21789] Hydronium_distance CV

bijaya pathak bijayapathak85 at gmail.com
Mon Sep 1 14:02:03 UTC 2025
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Dear Marcella  and Ivan , 
I have been trying to do the above simulation for sometimes now.  Setting 
values  hasn't been easy for the parameters. As per my understanding, I 
have tried a few possible values for the parameters. 
Sample input is given below. 
 &COLVAR
    &COORDINATION
      ATOMS_FROM 2                  
      ATOMS_TO 35     
      R0 2.6                       
      NN 6                         
      ND 12                        
    &END COORDINATION
  &END COLVAR
   &COLVAR
    &HYDRONIUM_DISTANCE
      OXYGENS 1..32            
      HYDROGENS 33..96        
      LAMBDA 20.0                  
      NH 2.2
      NN 0.56
      PF 6                        
      PM 8                        
      POH 6                      
      QF 12                       
      QM 16                        
      QOH 12                       
      ROH 2.6                   
    &END HYDRONIUM_DISTANCE
  &END COLVAR
I am only focusing on a O-H bond instead of the water molecule. So in 
coordination, I have defined a single H against O. Is that a problem ? 
Also, I am not sure if I have understood meanings of NH, PM and QM . I do 
not understand what is meant by M function. While in the original work, the 
M function is implemented in equation 3. Do we also need M function 
hydronium distance as well ? 
Any suggestions will be helpful. 
Sincerely 
Bijaya 

On Thursday, July 24, 2025 at 11:45:17 AM UTC+5:30 Ivan Gladich wrote:

> 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 <bijayap... 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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