On 14/04/2010 4:52 PM, PACIELLO GIULIA wrote:
Ok...so how could I know the energies among atoms?
Since it's not reported, you can't get breakdowns of energies. That's a
limitation from the use of GPU. If you want this information, perhaps do
your simulation on the GPU and re-rerun selected frames from your
trajectory on a different machine that does not use GPUs.
And how can I test if
my parallel code is running in the correct manner?
MD is chaotic. Tiny differences at an early stage lead to wildly
different results later. That's inevitable. However ensemble averages
should converge to the same value.
Do things converge to the same values? There's a chance that mdrun
-reprod will lead to equivalent total energies after only one step, if
that's been implemented that way.
Mark
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