From: Pijush Ghosh (pijush.ghosh_at_ndsu.nodak.edu)
Date: Mon Dec 06 2004 - 22:00:21 CST
I really appreciate the suggestions i am getting regarding my
problem. In response to what Obrien said i would like to mention that
I am using same seed for all
my runs and identical in the sense i am using running same configuration
file with different name may be with different or same number of
processors. I am running most of the runs for 400,000 thousands and this
variation in the results i am observing is terms of the final
coordinates of atoms.
Robert suggestd this could be because of some arithmatic operation
affecting round-off error.
Does NAMD for any of its calculation picks up some default random
number everytime it runs resulting some differernce in numerical
results, which should be theoretically zero though.
Any further discussion on this will be highly appreciated.
Edward Patrick Obrien wrote:
> What do you mean by identical conditions? Do you start these 3
>simulations from the same exact configuration? Do you use the same random
>number, or vary it?
>This info is needed to answer your questions.
>On Mon, 6 Dec 2004, Pijush Ghosh wrote:
>> 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
>> Any suggestions and references highly appreciated.
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