LINCS Warning or Freeze Behavior Depends on GROMACS Version

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GROMACS version: 2021.4, 2024.1, 2024.3, 2025.1
GROMACS modification: No

I ran the same protein simulation (Martini3-IDP force field, 20x20x20 box size, one protein+water+ions) on the Helios supercomputer (192 physical cores) using 4 versions of GROMACS: 2021.4, 2024.1, 2024.3, 2025.1, and each of them failed in a different way:

  • GROMACS 2024.1: Simulation stopped after approximately 1 minute with LINCS errors.

  • GROMACS 2024.3: Simulation stopped after approximately 2 hours with LINCS errors.

  • GROMACS 2021.4 and 2025.1: Simulations runs correctly for approximately 5 hours, then freezes without reporting explicit LINCS or any other errors.

The identical simulation ran successfully without any issue on my PC (8 physical cores), utilizing GROMACS version 2023.3.

I had exactly the same problem a year ago when I was running simulations using the Martini-3 force field in GROMACS on the LUMI supercomputer. At that time, I tried everything, but the only thing that helped was restarting the simulation in a loop:

for i in {1..10000}
do
gmx convert-tpr -s run$((i)).tpr -extend 200000 -o run$((i+1)).tpr
srun --exact -n1 -c 192 gmx mdrun -nt 192 -deffnm run$((i+1)) -cpi run$((i)).cpt -noappend
done

However, this approach does not help on the Helios supercomputer.
dynamic.mdp (1.7 KB)
AlfaGal3_solv_ionsP.top (469 Bytes)