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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