Hello All,
I have been doing membranes simulations using the computer nodes in UTEXAS
supercomputing center. Each board contains two Xeon Intel Duo-Core 64-bit
processors (4 cores in all) and nodes are interconnected with InfiniBand
technology.
The performance is great. However, I have got weird results if I increase
the number of processors more than 12. Even though the bilayer is still
intact, one or two lipids were popped out of the membrane not long after
the simulation was started.
To make sure that it is not the problem due to different initial
conditions,
I ran two separate md simulations starting from the same structure and
velocities on each atom but only with different number of processors, 8 and
16.
As expected, the job with 8 processors resulted in the intact membrane but
a lipid was pulled out of the membrane in the job run with 16 processors.
So far, I could not find out the cause of this problem.
Does anyone have any thought about this problem?
Thank you
Sunjoo
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