<div dir="ltr"><div>Hi,</div><div><br></div><div>RNAse is 18k/24k (dodec/cubic setup), otherwise you can stack the 5k villin and get 10k, 20k,... systems (using "gmx genconf -nbox N M K").</div><div><br></div><div>Additionally to water boxes, I do have some water + ethanol boxes too which do have bonded interactions, but that will only be useful if you really want the granularity of system sizes beyond what the villing stacking allows. I can share these if you are interested.<br></div><div><br></div><div>Cheers,<br></div><div><div><div dir="ltr" data-smartmail="gmail_signature">--<br>Szilárd</div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Fri, Jun 11, 2021 at 10:54 AM Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div>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>
</div>
<blockquote type="cite">
<div>
<p class="MsoNormal">Hello,<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">I would like to know if there are GROMACS
use cases/inputs that simulate about 50 – 2K atoms.
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Is there any benchmark hard coded in
GROMACS that allows parametrization and test different problem
sizes?
<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></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.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">The smallest case (ready to use) that I
found up to now is called “villin” with 5K atoms.<u></u><u></u></p>
<p class="MsoNormal"><u></u> <u></u></p>
<p class="MsoNormal">Thanks a lot, Guido.<u></u><u></u></p>
<p class="MsoNormal"><b><span style="font-size:10pt;color:rgb(102,102,102)"><u></u> <u></u></span></b></p>
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