Error of "There is no domain decomposition for 1 Ranks"?

User discussions
1

GROMACS version: 2022 and 2024

Dear Gromacs users:

I want to energy minimize a structure in Gromacs. When I run the simulation using mdrun option.

gmx grompp -f minim.mdp -c box.gro -o min.tpr
gmx mdrun -deffnm min -v -nt 4

I encounter with this error:

Fatal error:
There is no domain decomposition for 1 ranks that is compatible with the
given box and a minimum cell size of 15.5337 nm.
Change the number of ranks or mdrun option -rdd or -dds
Look in the log file for details on the domain decomposition

It is so strange. Because when I perform the simulation of the same system in nvt:

gmx grompp -f nvt.mdp -c box.gro -o nvt.tpr
gmx mdrun -deffnm nvt -v -nt 4

it proceeds without any error.

What is the main reason for that?

2

That doesn’t sound right and looks like a bug. Can you see in the log file where the distance of 15.5337 nm comes from?

3

Dear Hess,

Sorry for my late reply. I have attached the min.log file here. Please search for 16.3125 nm in the log file.

Thanks alot

min.log (14.3 KB)

4

The log file tells you what causes the issue:
two-body bonded interactions: 14.830 nm, Exclusion, atoms 28661 28702
multi-body bonded interactions: 14.830 nm, Angle, atoms 28661 28702
Minimum cell size due to bonded interactions: 16.312 nm

I guess you did something wrong in the setup of the initial coordinates which made bonded atoms separate by nearly 15 nm.

1 Like
5

Dear,

Thank you for your help.