GROMACS version:2019 doublé precision
GROMACS modification: Yes/No
Hello, I’m somewhat new to gromacs and found and issue i need some help with.
I´ve been running some NPT simulations on ionic liquids with success, recently ran in to the error “The domain decomposition grid has shifted too much in the Y-direction around cell 3 1 0. This should not have happened. Running with fewer ranks might avoid this issue.”
I tried looking into the manuals and online but I don’t think I’m understanding the issue.
Could someone explain what this error is about and what could cause it?
The error would indicate that your particles shift around a lot between the logical compartmentalisatoin that is used to speed up the simulations on multiple nodes.
Some guess what this error might indicacte:
- that you simulate very few particles on many nodes
- you might have some sorts of cavity developing in your system
- you might have extreme temperatures emerging in your system
If I understand correctly the particles move through the zone where they were originally placed at the start of the simulation, changing which processor is responsible for calculations on that particle. The problem would be that a processor has little or much to do triggering the error.
Certainly a difference between the job that failed and some of the successful ones is temperature, which i increased to match experimental data. Also checking the trajectories for cavities seems like a reasonable practice.