AMBER Archive (2005)

Subject: Re: AMBER: amber8 parallel sander

From: Carlos Simmerling (carlos_at_ilion.bio.sunysb.edu)
Date: Wed Jan 12 2005 - 06:38:30 CST

this is expected and OK since the order of operations differs with
different
numbers of CPUs and eventually introduces small changes into the dynamics.
the same would happen on different types of CPU. all of the trajectories are
equally acceptable.

yen li wrote:

> Hello amber
> I am testing the parallel version of amber8. I am running an md
> simulation over a small protein.
> I am testing the calculations on four, eight and sixteen processors.
> My problem is that, initially the energy values in the output files
> are the same, but as the simulation proceeds, the values start to
> diverge making the differences large. Is this kind of behaviour ok or
> do i need to take care of some parameters.
> Thanks
>
>
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