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

[Tsjerk Wassenaar]

Hi Yun,

For comparison, the conditions have to be equal. That does not include
possible hardware issues. So you should be fine.

Cheers,

Tsjerk

On Oct 11, 2011 4:41 AM, "Yun Shi" <yunshi09 at gmail.com> wrote:

Hi Justin,

I guess you are right, that some processors on that cluster appear to be
much slower than others.

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.

Thanks,
Yun

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