Coordination Collective Variable: Report but don't spawn hills

[Christopher O'Brien]

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


-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20150511/b8fb2e79/attachment.htm>