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

Guido Giuntoli guido.giuntoli at huawei.com
Wed Jun 9 17:38:04 CEST 2021


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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