From: Dong Luo (us917_at_yahoo.com)
Date: Tue Mar 27 2007 - 10:28:54 CDT
Parallel simulation in NAMD is based on space
division, which won't be a problem for large systems.
However, when dealing with small system like a short
peptide in water box, running the simulation with more
than 32 cpus may not get a good space distribution.
Based on my experience of heat annealing simulation of
a 22 residue peptide in water box, the system exploded
easily on 32 cpus, but stay quite stable with only one
cpu.
My question is that is there a rough relationship
between system size and cpu numbers that we can
follow?
Dong Luo
Department of physiology and biophysics
Boston University
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