Fwd: FEP slowdown during execution

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sat May 12 2018 - 01:12:35 CDT

I forgot adding that I am not observing such a slowdown with pure MD.
---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sat, May 12, 2018 at 8:10 AM
Subject: FEP slowdown during execution
To: NAMD <namd-l_at_ks.uiuc.edu>

I am nearly always observing a slowdown of FEP. during execution on a
NextScale cluster. A considerable slowdown: in the last simulation, on a
single node (36cores), from 0.0025s/step to 0.0060s/step. As such a
degradation of performance occurs variably from the first window to later
windows, while the FEP has to be carried out entirely, it becomes
problematic setting up the calculation, also because I am trying to have as
many steps as possible with alchequil and FEP.

I wonder whether the same problem has been ever observed.

Thanks for sharing experience.

francesco pietra

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