[gmx-users] OpenMM

Mark Abraham 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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