[CPMD-list] isolated molecule translation during dynamics

[Ari P Seitsonen]

Dear Yong,

   How did you assign the initial velocities, by hand or by giving an 
initial temperature? Could you please also provide your input file, it 
seems very strange that the molecule would translate that much.

     Greetings from Trieste,

        apsi

-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-=*=-
   Ari P Seitsonen / Ari.P.Seitsonen at iki.fi / http://www.iki.fi/~apsi/
   IMPMC, CNRS & Université Pierre et Marie Curie
   Tel: +33-1-4427 7542, Fax: +33-1-4427 3785, GSM: +33-6-6736 3820

On Mon, 22 Jan 2007, Yong Zhang wrote:

> 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
>> 
>> ===========================================================================
>> 
>