[CP2K:1353] Periodic MD

Fawzi Mohamed fa... at gmx.ch
Tue Sep 30 09:51:42 UTC 2008

On Sep 27, 2008, at 3:21 PM, ilya wrote:

> Dear users and developers,
> keyword "only applies to the generation of the pair lists" and as i
> understand it doesn't deal with motion. So when I run my MD sim for
> several hundreds of ps at high temperature the water molecules just
> fly away from the center even when everything PERIODIC is set to XYZ.
> I didn't find a method to constrain a system to the box. For example
> some apps can do something like this: when one molecule crosses the
> border it appears on the other side of the box. So may I constrain the
> system so it will not evaporate?

your system does not evaporate if it is periodic, the periodic copies  
interact as they should.

It is true that the coordinates are not wrapped in the initial cell,  
but this is done on purpose:

1) when everything is periodic putting a particle in the central cell  
or in one of its periodic copies in the other cells is exactly the  
same thing

2) wrapping the coordinates is easy (just do a modulo 1 in reduced  

3) non wrapping make the trajectory of a particle continuos in the  
normal space (no need of berry phase or something like it to remove  
the apparent jumps), this is very useful for example if you want to  
calculate diffusion.


> Is CP2K_INPUT / MOTION / FLEXIBLE_PARTITIONING a way to constrain the
> system (as I understand we can construct a spherical constrain around
> a CENTRAL_ATOM using it??) ??
> Thanks a lot,
> Ilya.

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