Fatal error:
There is no domain decomposition for 4 nodes that are compatible with the given box and a minimum cell size of 6.75605 nm
Change the number of nodes or mdrun option -rdd
Look in the log file for details on the domain decomposition
I used the option "-nt 1" to make it work. Sometimes the simulation is too small to be divided. :-)
A minimum DD cell size of 6.75 nm indicates that either you are using some long distance restraints (in which case you need fewer DD cells or you cannot run in parallel) or there is something terribly wrong with the topology. The DD cell size is based on bonded interaction distances, cutoffs, and a few other factors.
The error shouldn't depend on the force field. Something else has gone wrong, but without a complete list of your exact commands and the .log file itself from the failing run, it's impossible to guess at what the issue is. Any other warnings or errors from GROMACS tools would be helpful to know about.
What system are you trying to model? I had before similar error so maybe I can help you.
I have a question about this error. my system contains graphene and surfactants. In last box I put graphene in the middle of my box and the graphene was npbc and the mdrun went well, then I put a pbc graphene and the x and y dimension box fixed to match the size of graphene sheet. but in energy minimization step. I get this error! Can I put the x, y dimension of my box larger than pbc graphene?
Command line:
gmx mdrun -v -deffnm em
Fatal error:
There is no domain decomposition for 32 ranks that is compatible with given box and a minimum cell size of 3.21311 nm.
Why? :
Machine with large number of cores you might need to limit the number of threads, say with -nt 8
Solution:
Use following command line:
gmx mdrun -v -deffnm em -nt 8
Now program will be execute normally
I used the option "-nt 1" to make it work. Sometimes the simulation is too small to be divided. :-)
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