Issue with simulation instability along z-axis in protein-lipid systems

[FloK-uy]

Hello,
I would like to ask for some guidance.
I've been running simulations with POPC and a small protein. The simulation runs fine initially, but eventually it crashes along the z-axis.
I suspect the issue may be related to the fourierspacing = 0.2 setting in the .mdp file. In some cases, when I commented out this line, the simulation could be restarted and ran successfully.
I would like to know if this is an appropriate approach or if there is a recommended value for fourierspacing that I should use instead.

Thank you in advance,
Florencia

[MartinSonora]

Hi Florencia,

Thanks for reaching out.

Your observation is very insightful — the fourierspacing parameter can indeed influence the stability of PME electrostatics, particularly in systems with membranes or anisotropic like yours. This parameter defines the grid spacing for PME electrostatics: lower values increase accuracy but can also result in higher computational load.

By commenting out the fourierspacing line in your .mdp file, GROMACS reverts to its default value of 0.12, which is often more stable than 0.2 in membrane-protein simulations. This likely explains why your simulation could resume and run successfully after removing the line.

So yes, your approach makes sense — and I’d suggest explicitly setting fourierspacing = 0.12 in your .mdp to avoid ambiguities and ensure stability. In general, values between 0.12 and 0.16 are a good range for most biomolecular systems.

Best,

Martín