On 11/10/2011 1:40 PM, Yun Shi wrote:
Hi Justin,
I guess you are right, that some processors on that cluster appear to
be much slower than others.
More likely is that the mapping of processes to processors is faulty, as
Justin said.
But I am still wondering that, would the difference in initial maximum
inter charge-group distances (0.451 nm vs 0.450 nm) and minimum
initial size of DD gird (0.620nm vs 0.618nm) make the two simulations
NOT comparable? Because I want to compare the interactions of two
different ligands with the same protein.
That's just a detail of how the simulation is being implemented in
parallel. There are a vast number of algorithmically equivalent ways to
do this, and the initial conditions determine which is chosen. Since
your initial conditions differ, so do the details.
Mark
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