[CP2K:7069] Pulling molecule out of surface

Ralph Koitz ralph... at gmail.com
Tue Oct 20 10:14:24 CEST 2015


Hi,

Yes, you can define the point-plane distance also with respect to the
center of mass of some atoms.
See
http://manual.cp2k.org/trunk/CP2K_INPUT/FORCE_EVAL/SUBSYS/COLVAR/DISTANCE_POINT_PLANE/POINT.html

It should look something like this
&COLVAR
  &DISTANCE_POINT_PLANE
    ATOMS_PLANE 2 3 5
    ATOM_POINT 1
    &POINT
      TYPE GEO_CENTER
      ATOMS   7 3 1 6                !your phosphate...
    &END POINT
  &END DISTANCE_POINT_PLANE
&END COLVAR

Best,
Ralph

On Tue, Oct 20, 2015 at 6:27 AM, TZU-JEN LIN <tzujen... at gmail.com> wrote:

> Dear all CP2K users
>
> I attempt to do a calculation for pulling phosphate or carbonate out of
> mineral surfaces by metadynamics.
> I checked the manual of CP2K, it looks like there is no problem for
> pulling an ion out of a defined plane,
> because the collective variable is just the distance between the ion and
> defined plane.
> My question is that is it possible to define center of mass of a molecule
> as a collective variable ?
> Or I just can only pull phosphorus atom or carbon atoms of phosphate and
> carbonate respectively out of surface ?
>
> BEST,
> Tzu-Jen Lin
>
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-- 
Ralph Koitz
Binzm├╝hlestrasse 56
8050 Z├╝rich
ralph... at gmail.com
+41 78 600 2093
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