[gmx-developers] GROMACS uses cases with 50-2K atoms

Guido Giuntoli guido.giuntoli at huawei.com
Fri Jun 11 15:16:26 CEST 2021

Thanks Berk and Szilard,

I am trying to achieve a small system that stills being representative on a single core. If I understood correctly from: https://mailman-1.sys.kth.se/pipermail/gromacs.org_gmx-developers/2021-February/011004.html good scaling is achieved typically with setups of 50-1000 atoms/core in order to fit the problem in the LLC.

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?

Should I use https://manual.gromacs.org/documentation/2018/onlinehelp/gmx-solvate.html for generating water boxes?

Thanks a lot, Guido.

From: gromacs.org_gmx-developers-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-developers-bounces at maillist.sys.kth.se] On Behalf Of Szilárd Páll
Sent: Friday, June 11, 2021 2:55 PM
To: Discussion list for GROMACS development <gmx-developers at gromacs.org>
Subject: Re: [gmx-developers] GROMACS uses cases with 50-2K atoms


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").

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.


On Fri, Jun 11, 2021 at 10:54 AM Berk Hess <hess at kth.se<mailto:hess at kth.se>> wrote:

I don't think we have much else in that range.

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.



On 6/9/21 5:37 PM, Guido Giuntoli wrote:

I would like to know if there are GROMACS use cases/inputs that simulate about 50 – 2K atoms.

Is there any benchmark hard coded in GROMACS that allows parametrization and test different problem sizes?

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.

The smallest case (ready to use) that I found up to now is called “villin” with 5K atoms.

Thanks a lot, Guido.

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