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

[Szilárd Páll]

Hi,

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.

Cheers,
--
Szilárd


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

> Hi,
>
> 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.
>
> Cheers,
>
> Berk
>
> 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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