GROMACS Domain Decomposition Errors in Protein-Membrane Simulation with Martini

mpapadourakis
Wed, 05 Mar 2025 10:13:48 +0000
General Topics in Molecular Dynamics

Hi all,

I am attempting to simulate a protein-membrane system (60x60x25) using GROMACS 2024.4 with the Martini3 force field in the NPT ensemble. However, I am encountering domain decomposition errors immediately after minimization during NPT equilibration:

Fatal error:
“One or more atoms moved too far between two domain decomposition steps. This usually means that your system is not well equilibrated.”

I have tried several approaches to resolve this issue, including:

Running the NPT equilibration directly on the protein-membrane system.

Equilibrating the membrane separately before incorporating the protein.

Reducing the timestep from 20 fs to 10 fs.

Using the -rdd flag with values of 1.6 and 1.8.

Setting tau_p = 12.

Despite these attempts, the issue persists. Notably, the same system with smaller dimensions (30x30x15) runs without any errors.

Do you have any suggestions on how to resolve this issue?

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