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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks Berk and Szilard,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I am trying to achieve a small system that stills being representative on a single core. If I understood correctly from:
<a href="https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2021-February/011004.html">
https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2021-February/011004.html</a> good scaling is achieved typically with setups of 50-1000 atoms/core in order to fit the problem in the LLC.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">I am wondering if the water boxes are still representative of this situation without including the bonded forces. Do they use the nbnxn_kernel and the pme computations
in a similar way as a normal use case?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Should I use
<a href="https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-solvate.html">
https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-solvate.html</a> for generating water boxes?<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks a lot, Guido.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span style="font-size:11.0pt;font-family:"Calibri",sans-serif"> gromacs.org_gmx-developers-bounces@maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces@maillist.sys.kth.se]
<b>On Behalf Of </b>Szilárd Páll<br>
<b>Sent:</b> Friday, June 11, 2021 2:55 PM<br>
<b>To:</b> Discussion list for GROMACS development <gmx-developers@gromacs.org><br>
<b>Subject:</b> Re: [gmx-developers] GROMACS uses cases with 50-2K atoms<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Hi,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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").<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Cheers,<o:p></o:p></p>
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<p class="MsoNormal">--<br>
Szilárd<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Fri, Jun 11, 2021 at 10:54 AM Berk Hess <<a href="mailto:hess@kth.se" target="_blank">hess@kth.se</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">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:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Is there any benchmark hard coded in GROMACS that allows parametrization and test different problem sizes?
<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"> <o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Thanks a lot, Guido.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;color:#666666"> </span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;color:#666666">Mobile: +49 15904451229</span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;color:#666666">Email:
<a href="mailto:guido.giuntoli@huawei.com" target="_blank">guido.giuntoli@huawei.com</a></span></b><o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span style="font-size:10.0pt;color:#666666"> </span></b><o:p></o:p></p>
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