Navigating mdrun Challenges in GROMACS Simulations - Part I

Welcome back to our GROMACS error resolution series! In this edition, we'll focus on common challenges encountered during the mdrun process. Let's explore these issues, decipher their meanings, and outline effective solutions to ensure smooth GROMACS simulations.

Error 12: Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested Fmax

Error Message:

Stepsize too small, or no change in energy. Converged to machine precision, but not to the requested Fmax

Possible Causes:

1. Energy minimization limit reached: mdrun has minimized the structure to the extent possible with current parameters.
2. High water content: For systems with significant water, achieving an Epot of -105 to -106 is reasonable for starting MD simulations.

Troubleshooting Steps:

1. Interpret Fmax: Focus on Fmax value, indicating the slope of the potential energy surface. Consider additional minimization if required for specific purposes.
2. Consider double precision: For further minimization, explore different energy minimization methods or enable double precision in GROMACS.

Error 13: Energy minimization has stopped because the force on at least one atom is not finite

Error Message:

Energy minimization has stopped because the force on at least one atom is not finite

Possible Causes:

• Atoms too close: Two atoms in the input coordinates are too close, causing infinite forces during minimization.

Troubleshooting Steps:

1. Check initial coordinates: Review input coordinates to identify atom pairs that are too close.
2. Soft-core potentials: Explore using soft-core potentials for minimizing systems with infinite forces.

Error 14: LINCS/SETTLE/SHAKE warnings

Error Message:

LINCS/SETTLE/SHAKE warnings

Possible Causes:

• Constraint algorithm failures: LINCS, SETTLE, or SHAKE warnings indicate issues with constraint algorithms during dynamics.

Troubleshooting Steps:

• Diagnose system stability: These warnings often signal fundamental issues with system stability. Address larger problems causing constraints to fail.

Error 15: 1-4 interaction not within cut-off

Error Message:

1-4 interaction not within cut-off

Possible Causes:

1. Large velocities: Atoms have very large velocities, possibly due to system instability.
2. Blowing up molecules: If using LINCS for constraints, earlier LINCS warnings might precede this error.

Troubleshooting Steps:

1. Equilibration and energy minimization: Ensure the system is well-equilibrated and perform energy minimization.
2. Check parameters: Review parameters in the topology file for validity.

Error 16: Simulation running but no output

Error Message:

Simulation running but no output

Possible Causes:

1. Simulation slowness: Output may be delayed due to slow simulations.
2. Simulation issues: Potential generation of not-a-numbers (NANs) can slow down calculations significantly.

Troubleshooting Steps:

1. Set GMX_LOG_BUFFER: Speed up output by setting GMX_LOG_BUFFER to 0.
2. Check for NANs: Monitor the simulation for NANs, indicating potential issues.

Error 17: Cannot do Conjugate Gradients with constraints

Error Message:

Cannot do Conjugate Gradients with constraints

Possible Causes:

• Energy minimization with constraints: Conjugate gradient algorithm cannot be used for energy minimization with constraints.

Troubleshooting Steps:

• Refer to the reference manual: Check the GROMACS reference manual for limitations on energy minimization with constraints.

Error 18: Pressure scaling more than 1%

Error Message:

Pressure scaling more than 1%

Possible Causes:

• Oscillating simulation box: Oscillations due to large pressures and small coupling constants can lead to system resonance and crashes.

Troubleshooting Steps:

1. Optimize equilibration: Ensure the system is well-equilibrated before applying pressure coupling.
2. Adjust pressure coupling constant: Increase tau-p to slow down the response to pressure changes.

Error 19: Range Checking error

Error Message:

Range Checking error

Possible Causes:

• Simulation instability: The simulation is blowing up, requiring better energy minimization, equilibration, or topology design.

Troubleshooting Steps:

• Improve simulation stability: Perform thorough energy minimization, equilibration, and validate topology parameters.

Stay tuned for Part II, where we'll continue our exploration of mdrun challenges in GROMACS simulations.