AMBER Archive (2002)

Subject: Re: removing rotational motion in MD

From: Stéphane Teletchéa (steletch_at_biomedicale.univ-paris5.fr)
Date: Thu Jan 10 2002 - 02:35:54 CST

Le Mercredi 9 Janvier 2002 19:54, Sanjeev B.S. a écrit :
> But this flag is ignored for both belly and periodic simulations, isn't
> it?
>
> On Wed, 9 Jan 2002, Stéphane Teletchéa wrote:
>
> Le Mercredi 9 Janvier 2002 18:41, Michael G Cooney a écrit :
> > Dear Amber users,
> >
> > I wondered if there is a variable that can be set to remove rotational
> > motions in MD simulations over long (>2 ns) times for molecules such as
> > DNA oligos that have correlation times in this range. Perhaps I missed
> > this in the Amber manuals but would very much appreciate any suggestions
> > if there is an easy way to do this.
> >
> > Thank you for your help.
> >
> > Sincerely,
> >
> > Michael G. Cooney
> > Postdoctoral Associate
> > Dept. of Chemistry
> > Georgia State University
> > Atlanta, GA 30303
>
> NSCM=x, where x is the number of steps, page 140 of amber6's manual. You
> need to use it with NDFMIN=6,
>
> Stef

It is what is written in the book, but when you apply it, you see :
check COM velocity, temp: 0.000000 0.00(Removed)
in the output file.
So i am not sure the transformation are applied or not, as no more
indications are provided. Without NSCM=x however, no such output is written.

Stef 

-- 
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Teletchéa Stéphane - CNRS UMR 8601
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