[gmx-users] Re: reasons for slow computation?

Mark Abraham 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 
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.


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