CONDITIONED_DISTANCE COLVAR

Marcella Iannuzzi marci... at gmail.com
Sat Nov 12 12:27:09 CET 2016


Hi Nitish,

yes this variable has been successfully used. 
It is meant to calculate the distance between one atom and one atom taken 
from another group of atoms.
To select the second atom, the coordination function is selected, i.e., the 
atom with the largest coordination number is selected.
Using an input like

    &COLVAR

       &CONDITIONED_DISTANCE

         ATOMS_DISTANCE  235

         KINDS_FROM N

         ATOMS_TO  235

         R0 [angstrom] 3.00000000E+00

         NN  10

         ND  16

         LAMBDA 100

       &END

    &END COLVAR


The distance is calculated between atom 235 and the N atom that has the 
largest coordination with atom 235, i.e., the closest to atom 235.


Kind regards

Marcella

On Friday, November 11, 2016 at 1:03:03 PM UTC+1, Nitish Govindarajan wrote:
>
> Hi everyone,
> I was wondering if anyone has tried using the conditioned distance as a CV 
> in a metadynamics run. I am trying to use this, but I have some questions 
> on how to define ATOMS_DISTANCE and also the output seems to not print 
> after the 1st SCF cycle run.
>
>       &CONDITIONED_DISTANCE
>
>       ATOMS_DISTANCE 6 2
>
>       ATOMS_DISTANCE 6 3
>
>       ATOMS_DISTANCE 6 4
>
>       ATOMS_DISTANCE 6 5
>
>       ATOMS_DISTANCE 6 7
>
>       ATOMS_DISTANCE 6 8
>
>       ATOMS_DISTANCE 6 9
>
>       ATOMS_DISTANCE 6 10
>
>       ATOMS_DISTANCE 6 11
>
>       ATOMS_DISTANCE 6 12
>
>       ATOMS_DISTANCE 6 13
>
>       ATOMS_DISTANCE 6 14
>
>       ATOMS_DISTANCE 6 15
>
>       ATOMS_DISTANCE 6 16
>
>       KINDS_FROM O
>
>       KINDS_TO H
>
>       LAMBDA -20
>
>       ND 32
>
>       NN 8
>
>       R0 [angstrom] 1.27
>
>       &END CONDITIONED_DISTANCE
>
>
> Thanks,
>
> Nitish
>
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