Mark.Abraham at anu.edu.au
Wed Apr 14 08:58:37 CEST 2010
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.
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