From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Fri Mar 02 2007 - 17:59:17 CST
Stern, Julie wrote:
> Hello,
> Have there been any studies or comparisons done regarding reproducibility of
> an MD result in amber vs. namd? If all the parameter options are set the same and
> the initial conditions are the same, are the algorithms in amber and namd implemented
> the same so that an exact trajectory would come out the same? Where do you suppose
> the differences would be?
There is no chance they would reproduce each other. Computer arithmetic
is only an approximation to the true arithmetic, as described here
http://en.wikipedia.org/wiki/Floating_point#Accuracy_problems. You would
not even expect neighbouring versions of the same software to reproduce
each other. Tiny differences magnify according to the butterfly effect -
MD simulations are chaotic systems.
They should sample the same ensemble however, and in the limit of long
simulations, their observables will be equal.
Mark
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