GROMACS version:
GROMACS modification: Yes/No
Here post your question
I have been trying to setup a simulation run with a ligand molecule which is frozen and restraints are also applied. After initial equilibration when I am trying to run the production simulation I am getting the following error “Fatal error:
There is no domain decomposition for 360 ranks that is compatible with the
given box and a minimum cell size of 2.95027 nm
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition”
After referring to previous posts, I reduced the number of cores and processors. But even after trying several times and using the minimum number of cores and processors, the error doesn’t go. However, if I try running in serial it runs (but slow). Surprisingly, the same system without the ligand runs perfectly fine. So maybe the problem is due to the ligand, but then it does runs in serial…
I have been trying for quite sometime now, any help to solve this issue is appreciated.
Thanks,
Soumya