Hydronium_distance CV

[bijaya pathak]

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]

Keywords

• HYDROGENS

• LAMBDA

• NH

• NN

• OXYGENS

• PF

• PM

• POH

• QF

• QM

• QOH

• ROH

Greatly appreciate any suggestions

Thanks

Bijaya

[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

[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

[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

[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

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[bijaya pathak]

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