Src/gromacs/ewald/pme_redistribute.cpp (line 305)

User discussions
1

Dear Friends,
First of all, I am an inexperienced user of the gromacs. I have received the below message from the HPC cluster. What can I do to fix it?
Thanks in advance for your help.

GROMACS version: gromacs/2024.1-oneapi2024
GROMACS modification: No

step 32913800, will finish Sat Jan 11 06:49:10 2025

step 32913854: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 32913854: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.

step 32913854: One or more water molecules can not be settled.
Check for bad contacts and/or reduce the timestep if appropriate.
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates
Wrote pdb files with previous and current coordinates

Program: gmx mdrun, version 2024.1
Source file: src/gromacs/ewald/pme_redistribute.cpp (line 305)
MPI rank: 4 (out of 110)
Program: gmx mdrun, version 2024.1

Source file: src/gromacs/ewald/pme_redistribute.cpp (line 305)
Fatal error:
19 particles communicated to PME rank 0 are more than 2/3 times the cut-off
MPI rank: 92 (out of 110)
out of the domain decomposition cell of their charge group in dimension x.

This usually means that your system is not well equilibrated.
Fatal error:
For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.4 documentation

5 particles communicated to PME rank 16 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
This usually means that your system is not well equilibrated.
Fatal error:
For more information and tips for troubleshooting, please check the GROMACS
website at Common errors when using GROMACS - GROMACS 2024.4 documentation

5 particles communicated to PME rank 16 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
Abort(1) on node 4 (rank 4 in comm 0): application called MPI_Abort(MPI_COMM_WORLD, 1) - process 4
This usually means that your system is not well equilibrated.

2

Just like your error message says, there are some bad contacts in your system. How does your system look? Are there any overlapping or unnaturally placed molecules? What timestep did you use? How did you equilibrate your system?

3

Hi, catherine, Thanks for the message. Using the append key with the mdrun command,
I am making a restart when meeting such a problem. For now, it goes well. I dont know if it is a real solution.

4

hi Sedsil, how did you resolve this? I am currently experiencing same problem

5

Hi newton,
I resolved it by doing a restart procedure in the slurm file.

newton via GROMACS forums <notifications@bioexcel1.discoursemail.com>, 10 Nis 2025 Per, 14:33 tarihinde şunu yazdı:

6

A big thank you.
I had to re-equilibrate more gently with lower step size and improve emtol