Coordination Collective Variable: Report but don't spawn hills

[Marcella Iannuzzi]

 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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