Dear Dr Schwieters
I am a bit confused abt the scaling of EnsembleSimulation.
Your excellent paper in JACS ("How much backbone motion in ubiquitin...")
states that "calculation time approximately scales as the inverse of the
number of CPUs, upto Ne on multiple processor shared memory hardware". Does
this mean that if 1-member ensemble takes 1 hour, 2-member ensemble is
expected to take 2 hrs ? or does it mean 0.5 hrs or 1 hour?
I have a severe case of slowdown in which single member takes 3 min and
2-member takes 1 hr for 1 ps simulation ! This is because the stepsizes in 1
are much larger than in 2.
Then I ran the eginput/gb3_ensemble/tor_cross_two_all.py with ensembleSize 1
and 2, and got back 10 min and 30 min.
Do you expect this behaviour, or there could be doing something funny with
how I am running xplor-nih or the hardware?
Thanks,
Swanand Gore
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