[gmx-users] Re: reasons for slow computation?
Mark.Abraham at anu.edu.au
Tue Oct 11 04:48:29 CEST 2011
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
> 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.
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