AMBER Archive (2009)

Subject: Re: [AMBER] production run terminates due to (*) symbols in xxx.rst

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Thu Feb 05 2009 - 04:58:26 CST

Thanks for your suggestions.
I submitted the jon using iwrap=1.
Wating for the simulation run and finish.

Regards
Vijay

Vijay Manickam Achari
(Phd Student c/o Prof Rauzah Hashim)
Chemistry Department,
University of Malaya,
Malaysia
 vjramana_at_gmail.com

--- On Thu, 5/2/09, vallespardojl_at_chem.leidenuniv.nl <vallespardojl_at_chem.leidenuniv.nl> wrote:

> From: vallespardojl_at_chem.leidenuniv.nl <vallespardojl_at_chem.leidenuniv.nl>
> Subject: Re: [AMBER] production run terminates due to (*) symbols in xxx.rst
> To: amber_at_ambermd.org
> Date: Thursday, 5 February, 2009, 6:28 PM
> Dear Vijay,
>
> This symbols are usually because you have big values of
> something (if is in the restart file I suppose that
> coordinate or velocities values), and I suppose (I don't
> know what kind of job are you doing) that is because the
> your molecules are moving in all the space and the
> coordinates are in absolute values. In this case you have
> two options:
>
> * You can use the IWRAP option in the input file, this
> option is for have the coordinates always inside of a
> boxsize instead in absolute values.
> * The other option is run a smaller job (in order to avoid
> this *** values), rescale the values with the
> "ptraj" program and put again the job.
>
> I hope give you helpful tips,
>
> Jose Luis
>
>
>
>
> Quoting Vijay Manickam Achari <vjrajamany_at_yahoo.com>:
>
> > Dear Amber Users,
> >
> > My production run terminates due to (*) symbols in
> xxx.rst file.
> > What shall I do to continue to run the production?
> >
> > Thank you.
> > Vijay
> >
> > Vijay Manickam Achari
> > (Phd Student c/o Prof Rauzah Hashim)
> > Chemistry Department,
> > University of Malaya,
> > Malaysia
> > vjramana_at_gmail.com
> >
> >
> >
> >
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER_at_ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
>
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