[CPMD-list] isolated molecule translation during dynamics

[Yong Zhang]

Thanks for all these suggestions. I am testing the SUBTRACT keyword now.

For the symmetry=0 or 1, the manual says, "for many systems using a large
enough cell and pbc is also an option. ...except in difficult cases such as
charged molecules..." and "the pbc calculation is always cheaper for a box
of the same size". Because I have a neutral molecule, I expect similar
results by using either symmetry=0 or 1. But, to be honest, I do not have
special reason to perfer one over the other. And actually, I do  not really
know the advange or disadvantage of one over the other one, especially for
my system. I appreciate if you or anyone can put more comments on this.

Thanks.
Yong


On 1/22/07, Nisanth Nair <nisanth.nair at theochem.ruhr-uni-bochum.de> wrote:
>
> Hi
> One more thing; use also SYMMETRY 0 for isolated molecule. See more
> details in
> the manual.
> cheers,
> Nisanth
>
> On Sunday 21 January 2007 14:12, Juerg Hutter wrote:
> > Hi
> >
> > check the manual for the keywords
> >
> > SUBTRACT COMVEL
> > SUBTRACT ROTVEL
> >
> > regards
> >
> > Juerg Hutter
> >
> > ----------------------------------------------------------
> > Juerg Hutter                   Phone : ++41 44 635 4491
> > Physical Chemistry Institute   FAX   : ++41 44 635 6838
> > University of Zurich           E-mail: hutter at pci.unizh.ch
> > Winterthurerstrasse 190
> > CH-8057 Zurich, Switzerland
> > ----------------------------------------------------------
> >
> > On Sat, 20 Jan 2007, Yong Zhang wrote:
> > > Hi,
> > >
> > > I am running BOMD on a isolated, neutral, small molecule (with
> dimension
> > > < 5A). I used symmetry=1 with a "large enough cell" of 12A. No" NOSE"
> was
> > > used. I found the molecule translated a lot during the MD: the
> molecule
> > > was at the center of the box (0,0,0) in the beginning, but the
> > > coordinates changed to something like (-80, 95, -130) after a while,
> > > which is much larger than the box dimension. I checked the molecule
> > > structure, it seems ok. But will this cause any problem? Is there a
> way
> > > to remove this translation?
> > > Thanks
> > >
> > > Yong
> >
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> > CPMD-list at cpmd.org
> > http://cpmd.org/mailman/listinfo/cpmd-list
>
> --
>
> ===========================================================================
> Nisanth N. Nair
> Lehrstuhl fuer Theoretische Chemie   Tel: ++49 (0)234 32 22121
> Ruhr-Universitaet Bochum                Fax: ++49 (0)234 32 14045
> Universitaetstrasse 150
> D-44801 Bochum, Germany
> Email: nisanth.nair at theochem.ruhr-uni-bochum.de
> Web  : http://www.theochem.ruhr-uni-bochum.de
>
> ===========================================================================
>
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