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
My question is that is there a rough relationship
between system size and cpu numbers that we can
Department of physiology and biophysics
TV dinner still cooling?
Check out "Tonight's Picks" on Yahoo! TV.
This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:20:07 CST