From: Edward Patrick Obrien (edobrien_at_Glue.umd.edu)
Date: Mon Dec 06 2004 - 19:37:43 CST
Maybe I misunderstood you, but are you saying that different random
number seeds will still result in trajectories behaving in the same way?
On Tue, 7 Dec 2004, [iso-8859-1] Jérôme Hénin wrote:
> As far as I know, two runs using exactly the same simulation parameters and
> starting point, run on the same machine, and without Langevin dynamics (or
> specifying the seed for the pseudo-random generator), should behave exactly
> the same way, because the machine itself is supposed to be deterministic.
> If any of the above criteria is not met, the two simulations are likely to
> differ very slightly after a few hundred steps, which is to say that they may
> be wildly different after an average-sized run.
> Does something in your experience go against this? If yes, I would be
> interested to read more about it.
> Le mardi 07 Décembre 2004 00:25, vous avez écrit :
> > NAMD Friends,
> > I have a question.
> > When we run simulations(optimisation or MD) for any
> > system under identical condition three times, we end up with results
> > which are not exactly same but
> > vary within a range, which we denote by error bar in the plot. My
> > question is inspite of everything remaining same, what could be the
> > possible reasons giving rise to
> > these differences in results? Is it because of computation error ? or
> > anywhere in calculation in NAMD any other parameters involved which
> > causes so.
> > Any suggestions and references highly appreciated.
> > Pijush Ghosh.
> Jérôme Hénin
> Equipe de Dynamique des Assemblages Membranaires
> Université Henri Poincaré / CNRS UMR 7565
> B.P. 239 54506 Vandoeuvre-lès-Nancy Cedex
> Tel : (33) 3 83 68 43 95 Fax : (33) 3 83 68 43 71
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