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<div class="moz-cite-prefix">Hi,<br>
<br>
I don't think we have much else in that range.<br>
<br>
I would use water boxes of different size. They don't have bonded
interactions, so you don't test everything, but it is anyhow
unrealistic to use a single thread, as synchronization between
threads and cache sharing have large effects on the performance of
GROMACS.<br>
<br>
Cheers,<br>
<br>
Berk<br>
<br>
On 6/9/21 5:37 PM, Guido Giuntoli wrote:<br>
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<p class="MsoNormal">Hello,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I would like to know if there are GROMACS
use cases/inputs that simulate about 50 – 2K atoms.
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Is there any benchmark hard coded in
GROMACS that allows parametrization and test different problem
sizes?
<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The nonbonded-benchmark helps but I need
something that executes all the typical GROMACS algorithms
(PME, NxN computations, etc.). I need such a small case for a
single-core simulator where I don’t have any threading
facility.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">The smallest case (ready to use) that I
found up to now is called “villin” with 5K atoms.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Thanks a lot, Guido.<o:p></o:p></p>
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