Resolving Atom Index Out-of-Bounds Errors in GROMACS

In the second blog of our GROMACS error resolution series, we'll delve into the "Atom index in bonds out of bounds" error and another related issue: "Atom index in position_restraints out of bounds." These errors often perplex users but can be addressed with careful consideration of topology file organization.

Error 2: Atom Index Out-of-Bounds in Bonds

Error Message:

Atom index (1) in bonds out of bounds
[ file spc.itp, line 32 ]
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.

Solution:

Check the topology file and ensure that each [moleculetype] section contains all the relevant data for that molecule, with no interference from other molecule types. Also, pay attention to the order of inclusion and the structure of #include directives.

Additional Issue: Atom Index Out-of-Bounds in Position Restraints

Error Message:

Atom index n in position_restraints out of bounds
A common problem is placing position restraint files for multiple molecules out of order. Recall that a position restraint itp file containing a [ position_restraints ] block can only belong to the [ moleculetype ] block that contains it.

Wrong topology file:

#include "topol_A.itp"
#include "topol_B.itp"
#include "ligand.itp"

#ifdef POSRES
#include "posre_A.itp"
#include "posre_B.itp"
#include "ligand_posre.itp"
#endif

Solution:

Organize the topology file to match the correct order of [moleculetype] sections and their associated #include directives. The atom index in each [position_restraint] block must be relative to the specific [moleculetype], not the system as a whole.

Topology File Correction:

#include "topol_A.itp"
#ifdef POSRES
#include "posre_A.itp"
#endif
#include "topol_B.itp"
#ifdef POSRES
#include "posre_B.itp"
#endif
#include "ligand.itp"
#ifdef POSRES
#include "ligand_posre.itp"
#endif

Explanation:

This correction highlights the importance of correctly structuring the topology file, especially when using #include directives. The revised layout ensures that position restraint files align with their respective [moleculetype] sections, preventing interpretation errors by GROMACS.

Common Causes:

1. Incorrect topology file structure: Mixing different [moleculetype] sections or misusing #include directives can lead to errors.
2. Position restraint misplacement: Placing position restraint files in the wrong order, affecting the correspondence with [moleculetype].

Possible Solutions:

1. Organize topology file: Ensure proper ordering and separation of [moleculetype] sections.
2. Check position restraint alignment: Validate that position restraint files align correctly with their respective [moleculetype] sections.
3. Follow documentation: Refer to the GROMACS documentation for correct syntax and structure of topology files.

Stay tuned for more insights into troubleshooting GROMACS errors in the upcoming blogs.