Unraveling Complex GROMACS moleculetype Errors

Welcome back to the latest addition to our GROMACS error resolution series. In this edition, we'll dive into four more common errors that users might encounter during molecular dynamics simulations. Let's dissect these issues and explore effective solutions.

Error 5: Fatal error: No such moleculetype XXX

Error Message:

Fatal error: No such moleculetype XXX

Possible Causes:

1. Missing moleculetype definition: The [ molecules ] section in the top file refers to a moleculetype (XXX) that is not defined in the top file or any included itp file.
2. Syntax or inclusion issues: Problems with #ifdef or #include statements might lead to incorrect parsing of moleculetype definitions.

Troubleshooting Steps:

• Check [ molecules ] section: Ensure that all moleculetypes referenced in the [ molecules ] section are defined earlier in the top file or included itp files.
• Verify syntax and inclusions: Review the syntax and proper inclusion of moleculetype definitions using #ifdef and #include statements.

Error 6: T-Coupling group XXX has fewer than 10% of the atoms

Error Message:

T-Coupling group XXX has fewer than 10% of the atoms

Possible Causes:

• Inefficient thermostat grouping: Specifying separate thermostats for every molecule type, especially with less than 10% of the atoms in a group, can lead to simulation inaccuracies.

Troubleshooting Steps:

• Optimize thermostat grouping: Aim for a more efficient thermostat grouping, possibly combining molecule types that appear together in the simulation. Consider using the default System group.

Error 7: Cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element

Error Message:

The cut-off length is longer than half the shortest box vector or longer than the smallest box diagonal element. Increase the box size or decrease rlist.

Possible Causes:

• Box dimensions issue: The dimensions of the simulation box result in an atom interacting with itself, violating the minimum image convention.

Troubleshooting Steps:

• Adjust box size or rlist: Increase the simulation box size to ensure it is at least twice the cut-off length in all dimensions, or decrease the cut-off length.

Error 8: XXX non-matching atom names

Error Message:

XXX non-matching atom names

Possible Causes:

• Mismatch between topology and coordinate file: The order of atoms specified in the [ molecules ] directive does not match the order in the coordinate file.

Troubleshooting Steps:

• Ensure topological consistency: Confirm that the [ molecules ] directive matches the exact order of atoms in the coordinate file.

Error 9: The sum of the two largest charge group radii (X) is larger than rlist - rvdw/rcoulomb

Error Message:

The sum of the two largest charge group radii (X) is larger than rlist - rvdw/rcoulomb

Possible Causes:

1. Charge group size: Charge groups encompass too many atoms, exceeding recommended sizes.
2. Incompatible mdp settings: Mismatch between mdp settings and chosen algorithms, especially for switch or shift functions.

Troubleshooting Steps:

• Optimize charge group size: Ensure charge groups consist of an appropriate number of atoms (ideally 4 or fewer).
• Check mdp settings: Adjust mdp settings to align with chosen algorithms and prevent missing interactions.

Error 10: Invalid line in coordinate file for atom X

Error Message:

Invalid line in coordinate file for atom X

Possible Causes:

• Broken gro file format: Issues with the gro file format, such as an incorrect number of atoms specified in the second line.

Troubleshooting Steps:

• Review gro file format: Check the gro file format for correctness, especially the number of atoms specified in the second line.

Error 11: Atom index (1) in bonds out of bounds (1-0)

Error Message:

Fatal error:

[ file spc.itp, line 32 ]
Atom index (1) in bonds out of bounds (1-0).
This probably means that you have inserted topology
section "settles" in a part belonging to a different
molecule than you intended to. In that case, move the
"settles" section to the right molecule.

Possible Causes:

• Topology misplacement: The topology section, e.g., "settles," is inserted in the wrong part of the molecule, causing index discrepancies.

Troubleshooting Steps:

• Review topology placement: Ensure that all [molecules] sections contain data specific to that molecule and are placed correctly. Avoid including another molecule type (itp file) before the previous [moleculetype] has ended.

By addressing these diverse GROMACS errors, users can enhance the robustness and accuracy of their molecular dynamics simulations. 

Stay tuned for more insights in our ongoing GROMACS error resolution series.