On Tue, 2014-05-20 at 20:56 +0800, Val Yu wrote:
> Thank you so much. I said it a problem because I was using the method in the
> following paper to predict enzyme activity:
>
> Wang, B.F. et al. Quantitative Structural Insight into Human Variegate
> Porphyria Disease. JOURNAL OF BIOLOGICAL CHEMISTRY 288, 11731-11740 (2013).
>
> It is a method based on geometry distribution statistics. I used pmemd
> instead of sander used in the paper. And I found I cannot reproduce
> prediction in two parallel simulations (for "parallel" I mean I run two
> simulations in the same supercomputers in the same time, but they used
> different CPUs of course).
> I used to think that pmemd was just a faster version of sander in parallel
> computation and the former can replace latter in any situation. It may be
> caused by inaccurate understanding of the sentence in amber manual "For the
> supported functionality, the input required and output produced (by pmemd)
> are intended to exactly replicate sander 9 within the limits of roundoff
> errors."
pmemd _can_ be used instead of sander -- they give identical results out
to machine precision. The nature of floating point precision means that
no two simulations are exactly reproducible in general. [1] You cannot
always expect to reproduce results in exactly the same timescale as
previous studies, but in the limit of infinite sampling they should
agree perfectly.
Hope this helps,
Jason
[1] Exact reproducibility is possible in very specific circumstances --
but typically requires using the same hardware and same version of
software if it is possible at all.
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue May 20 2014 - 07:00:02 PDT
