[CP2K-user] [CP2K:20523] Re: COORDINATION CV with restrictions

[T deJ]

Hi Tugwell,

You can constrain a coordination number (CN) CV with the CONSTRAINT section 
under MOTION and the COLVAR section in FORCE_EVAL/SUBSYS, The COLVAR 
section can be specified as follows:

  &COLVAR
    &COORDINATION
       ATOMS_FROM ${your_c_index}
       ATOMS_TO ${atom1_index} ${atom1_index} ! etc. Space separated
       ! or
       ! KINDS_TO H C
       ! 
       NN ${your_value}
       ND ${your_value} 
       R0 ${your_value} 
    &END COORDINATION
  &END COLVAR

Where DN, NN, and R0 should be declared to adapt the switching function to 
your needs. You may well want to have 2 different switching functions for 
C-C and C-H bonds. You can do this by, e.g., combining 2 CN CV with the 
COMBINE_COLVAR function:

  &COLVAR
    &COMBINE_COLVAR
      &COLVAR ! Internal CV1
          ...
      &END COLVAR
      &COLVAR ! Internal CV2
          ...
      &END COLVAR
      FUNCTION CV1 + CV2 ! Combine the previously defined CVs
      VARIABLES CV1 CV2
     &END COMBINE_COLVAR
  &END COLVAR

Note that the internally defined CVs do not count toward the global COLVAR 
numbering

The CV can then be constrained or restrained in the constraint section as 
follows:

&MOTION
  &CONSTRAINT
    &COLLECTIVE
      COLVAR 1 ! COLVARS are numbered in the order they  were defined
      INTERMOLECULAR ! Presumably what you need
      TARGET 2 ! !!! This will be dependent of your definition of the 
switching function and your purposes
    &END COLLECTIVE
  &END CONSTRAINT
...
&END MOTION

The lagrange multipliers can be accessed by adding the 
&LAGRANGE_MULTIPLIERS subsection in &COLLECTIVE if you want to do 
Bluemoon-based thermodynamic integration.

If you only wish to prevent the carbene from coordinating, you could also 
use the LOWERWALLS functionality of Plumed (integrated within CP2K during 
compilation with certain flags).
As a final note, choosing the CN CV with too many atoms (e.g. through the 
use of KINDS_TO) may cause the SHAKE algorithm, which constrains the CV, to 
not converge.

Best,
Tjeerd
On Monday 29 July 2024 at 16:31:03 UTC+2 T. Tugwell wrote:

> Hi all,
> I am trying to run AIMD where I want to assign a CV of coordination number 
> to a carbene carbon. I then want to limit the coordination number to almost 
> all other carbons or hydrogens in the system. Does anyone know how this can 
> be done in cp2k?
> Best,
> Thomas
>

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