Coordination Collective Variable: Report but don't spawn hills

[Christopher O'Brien]

Thanks for the reply.

I believe that I should clarify the matter at hand. The Coordination COLVAR 
starts very near zero, but it should since the F is still attached to the 
rest of the molecule. It is only after the F detaches that the waters will 
actually be able to solvate the F ion. My concern is that the potential 
well that the solvated F ion resides in is being filled by the gaussians 
and preventing the solvation from occurring after F has moved away from the 
molecule. The study I am trying to replicate used the coordination as a 
collective variable (Unfortunately, the authors won't respond to my 
queries). The study offers a lot of details and not mention they did 
anything out of the ordinary. I am curious why even after 10ps I don't see 
the solvation occurring despite it being driven to occur. But my concern is 
that it might be driven away from the solvated state. 

On Monday, May 11, 2015 at 2:43:14 PM UTC-6, Marcella Iannuzzi wrote:
>
>  Hi Cristopher,
>
>   It is possible that the MTD potential is pushing your system too fast 
> away from equilibrium, without allowing the correct reorganisation of the 
> solvent. This happens when the hills are too large and new hills are added 
> too frequently. 
> Difficult to be more specific and guess which COLVAR is responsible 
> without having the output, but  if the coordination with Ow does not 
> change, it is not the coordination that is driving the system. 
> The FES is reconstructed using the hills building up the MTD potential. 
> These latter are defined in terms of the COLVARs used for the MTD.
> You can define more COLVARs and use only some of them as METAVARs, though. 
> The additional COLVARs obviously play no role in MTD and their values are 
> not recorded in the MTD output files. 
> Anyway structural parameters can be monitored from the post processing of 
> the trajectory. 
>
> Kind regards
> Marcella
>
> On Monday, May 11, 2015 at 9:05:24 PM UTC+2, Christopher O'Brien wrote:
>>
>> I am attempting to study the FES for a SN2 reaction (i.e. a negative ion 
>> (F-) leaves the molecule and becomes solvated, while an OH- takes its 
>> place). In attempting to reproduce the results of an article using CP2K's 
>> metadynamics, I am seeing the F being driven away from the molecule, but 
>> not seeing it being solvated. I presently have the COLVARS declared as 
>> below. 
>>
>> I have two concerns:
>> 1.) Is the coordination COLVAR driving the O in water away from the F ion?
>> 2.) Is there a way to have the COLVAR show up in the free energy surfaces 
>> generated by the fes.sopt code but not be used with hills? Simply leaving 
>> the coordination COLVAR out of the motion section, but still declared in 
>> the &SUBSYS section eliminated it from the FES generated by the fes.sopt 
>> program altogether.
>> &MOTION
>>   &FREE_ENERGY
>>
>>
>>    METHOD METADYN 
>>
>>
>>    &METADYN 
>>
>>     DO_HILLS .TRUE. 
>>
>>     WW [hartree] 1.0E-2 
>>
>>     NT_HILLS 15 
>>
>>
>>    &METAVAR 
>>
>>      COLVAR 1 
>>
>>      SCALE 0.08 
>>
>>     &END METAVAR 
>>
>>
>>     &METAVAR 
>>
>>      COLVAR 2 
>>
>>      SCALE 0.08 
>>
>>     &END METAVAR 
>>
>>
>>     &METAVAR 
>>
>>      COLVAR 3 
>>
>>      SCALE 0.08 
>>
>>     &END METAVAR
>>   &END FREE_ENERGY
>> &END MOTION
>> and in the &FORCE_EVAL section as:
>>   &SUBSYS
>>
>>      &CELL 
>>
>>       ABC 12.97658 12.90794 12.97688 
>>
>>       PERIODIC XYZ 
>>
>>     &END CELL 
>>  
>>
>>     &COLVAR 
>>
>>      !P to F
>>  
>>      &DISTANCE 
>>
>>       ATOMS 12 18 
>>
>>      &END DISTANCE 
>>
>>     &END COLVAR 
>>
>>
>>     &COLVAR 
>>
>>      !P to O 
>>
>>      &DISTANCE 
>>
>>       ATOMS 12 13 
>>
>>      &END DISTANCE 
>>
>>     &END COLVAR 
>>  
>>
>>     &COLVAR 
>>
>>      !see 10.1021/jp301490k for ND NN R0 parameter meaning 
>>
>>      ! P to O in water 
>>
>>      &COORDINATION 
>>
>>       ND 12 
>>
>>       NN 6 
>>
>>       R0 [bohr] 3.0 
>>
>>       KINDS_FROM P 
>>
>>       KINDS_TO Ow 
>>
>>      &END COORDINATION 
>>
>>     &END COLVAR
>>
>>     &COORD
>>       ...    
>>     &END COORD
>>
>> &END SUBSYS
>>
>>
>>
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