[AMBER] Wanna run nanoseconds of QM/MM MD?

From: yunshi11 . <yunshi09.gmail.com>
Date: Fri, 22 Nov 2013 10:19:34 -0800

Dear all,

I have a enzyme-substrate system that includes 80 QM+link atoms (with PM3,
TIP3P water, PME implemented).

As suggested in Amber12 manual, the scaling of such calculations are not
good. In my test, both 24-core run and 12-core run gave me 20 ps per day,
which means 50 days for 1 ns. Thus I wonder how to improve the performance.

Should I adjust the number of cores according to the number of QM/link
atoms? It seems kind of inefficient that NO QM atoms have been assigned to
4 of the 24 cores, while the other 20 cores take 4 QM atoms each.

How about using GPUs?

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Received on Fri Nov 22 2013 - 10:30:03 PST
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