FEP & node/core number

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Mon Apr 30 2018 - 10:36:26 CDT

In the frame of ligand-protein FEP, the system (total 50,555 atoms) was MD
equilibrated along 12ns on two nodes (72 cores).

With the same hardware, or six node (216 cores), FEP immediately crashed
because of protein atoms moving too fast.

With four nodes (144 cores) the trial (10 min) arrived safely to step
72,000, with performance 0.09days/ns.

All three simulations above were repeated with identical results.

I am curious about that, as in the recent past I was already sporadically
faced by FEP problems of atoms moving too fast (at the fist step, like in
the case above) for ligand-protein systems that had been accurately
equilibrated. At that time I did not try to change the number of

Memory was more than enough in all cases.

Thanks for paying attention to that.

francesco pietra

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