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

Berk Hess hess at kth.se
Fri Jun 11 10:53:52 CEST 2021


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:
> Hello,
> 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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