Navigating mdrun Challenges in GROMACS Simulations - Part II

Error 20: X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

Error Message:

X particles communicated to PME node Y are more than a cell length out of the domain decomposition cell of their charge group

Possible Causes:

• System blowing up: Indicates particles moving across the system, leading to a severe problem.

Troubleshooting Steps:

• Check system integrity: Investigate the system trajectory to identify and fix issues leading to particle movement.

Error 21: A charge group moved too far between two domain decomposition steps

Error Message:

A charge group moved too far between two domain decomposition steps

Possible Causes:

• Insufficient equilibration: System not equilibrated sufficiently before using pressure coupling.

Troubleshooting Steps:

1. Observe system trajectory: Monitor the system trajectory to identify problematic parts of the structure.
2. Adjust pressure coupling: Increase tau-p to slow down the response to pressure changes.

Error 22: Software inconsistency error: Some interactions seem to be assigned multiple times

Error Message:

Software inconsistency error: Some interactions seem to be assigned multiple times

Possible Causes:

• Simulation issues: Interactions assigned multiple times indicate a software inconsistency, potentially arising from system problems.

Troubleshooting Steps:

• Review system setup: Check the system setup and structure for errors leading to software inconsistencies.

Error 23: There is no domain decomposition for n ranks that is compatible with the given box and a minimum cell size of x nm

Error Message:

There is no domain decomposition for n ranks that is compatible with the given box and a minimum cell size of x nm

Possible Causes:

• Parallel calculation issues: Unable to partition the simulation cell into chunks for parallel calculations.

Troubleshooting Steps:

1. Review charge group size: Large charge groups may contribute to the issue. Consider adjusting charge group sizes.
2. Check nst parameters: Ensure nst parameters in the mdp file are set appropriately.
3. Parallel calculation awareness: If not intending to run a parallel calculation, use the -ntmpi 1 option to prevent thread-based parallelism.

By addressing these mdrun challenges in GROMACS simulations, users can enhance the reliability and efficiency of their molecular dynamics studies. Stay tuned for more such series. Do let us know in comments if your error is not mentioned in our series.