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

Yun Shi yunshi09 at gmail.com
Tue Oct 11 18:48:36 CEST 2011

Hi Mark,

I am not quite sure. While the "details" are different, I guess it is still
valid to compare some statistical properties, right? For example, I should
still be able to compare the average COM distance of these two ligands over
long trajectories, and make the conclusion that one is better than the other
since the distance is smaller. So should I be able to compare any averaged,
or say, clustered properties?


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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