Fatal Error: no domain decomposition for rank 4, min cell size 1.776 nm

User discussions
1

GROMACS version:2022.4
GROMACS modification: Yes/No
I am trying to run free energy calculation for the 20 standard amino acids. My simulations ran fine for smaller amino acids like glycine, but I’m having this issue with tryptophan, phenylalanine, and tyrosine. I am having trouble on the larger amino acids and getting this fatal error:

There is no domain decomposition for 4 ranks that is compatible with the given
box and a minimum cell size of 1.77637 nm.

In other discussion I have seen people running too many ranks and I have tried my mdrun with 2 ranks and still get this issue. The box side length I am using is 3.23536 nm

I can sucessfully run energy minimizations, npt, and nvt but get this error when atempting the production run. In these runs I also disabled the free energy calculation and tried to just run the simulation.

2

You likely have exclusions over long distances due to decoupling a large molecule. But for such a small system using multiple domains is never going to be faster. Use 1 MPI rank and multiple OpenMP threads.