Periodic MD

[ilya]

Fawzi and Axel, thanks for more clarifications!

Ilya.


On Sep 30, 6:00 pm, Axel <akoh... at gmail.com> wrote:
> On Sep 30, 5:51 am, Fawzi Mohamed <fa... at gmx.ch> wrote:
>
>
>
> > On Sep 27, 2008, at 3:21 PM, ilya wrote:
>
> > > Dear users and developers,
>
> > > as the doc says CP2K_INPUT / FORCE_EVAL / SUBSYS / CELL / PERIODIC
> > > 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
> > units)
>
> to add to this:
> if you write trajectories in .dcd format, it is as easy as
> calling "pbc wrap" in VMD to get the molecules wrapped back
> into the principal unit cell. there are several ways to do this
> (by atom, by residue, by chain) and thus it is a good idea to
> store coordinates "unwrapped" so that one can wrap them back
> in the preferred way. unwrapping a previously wrapped trajectory
> is far more error prone and complicated. for details see:http://www.ks.uiuc.edu/Research/vmd/plugins/pbctools/
>
> the .dcd format is needed as it stores the unit cell information,
> otherwise you have to use "pbc set" to set the box manually.
> heers,
>    axel.
>
>
>
> > 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.
>
> > Fawzi
>
> > > 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.