Thanks for your detailed question — this is a common issue when dealing with distance restraints in GROMACS, especially when working with atoms that are not covalently bound and may even be in different molecules or groups.

Let me walk you through what the error means, how distance restraints work in GROMACS, and how you can fix it step by step.

🧨 Your Error Explained

Atom index (2) in distance_restraints out of bounds (1-1).

This means GROMACS only sees 1 atom in the molecule where you've defined the distance_restraints, but you're referencing atom index 2 — which doesn’t exist in that section of the topology.

🧪 What Causes This?

This error usually occurs when:

🧰 How to Fix It

✅ Step 1: Determine the Two Atoms You Want to Restrain

• Are they from the same molecule or different molecules? If from the same molecule, the restraint can go inside that molecule’s topology. If from different molecules, special handling is needed.

✅ Step 2: Restraint Between Atoms in the Same Molecule

If atoms are in the same [ moleculetype ] (e.g., residues of a protein or nucleic acid):

[ distance_restraints ] ; ai aj type index type' low up1 up2 fac 1 2 1 0 1 0.5 0.6 0.7 1.0

• ai, aj = local atom indices (check .itp file)
• type = 1 for standard restraint
• low, up1, up2 = distance bounds

Make sure you include this .itp file properly in your .top file.

✅ Step 3: Restraint Between Atoms in Different Molecules

This is your case!

GROMACS does not allow distance_restraints between atoms in different molecules directly in the topology file. To work around this, you have two options:

🛠️ Option 1: Merge the Two Molecules into One Moleculetype

If the two atoms are in different molecules, but you want to apply restraints:

• Combine both molecules into one [ moleculetype ] block.
• Define both atoms within that new single molecule.
• Use distance_restraints with local atom indices.

⚠️ This is feasible only if you can logically merge them (e.g., protein + ligand, or two peptides being simulated together).

🧼 Option 2: Use Plumed with GROMACS for Intermolecular Distance Restraints

Plumed is a plugin for enhanced sampling and collective variable-based restraints.

You can restrain the distance between any two atoms, even across molecules, using Plumed.

Example (in plumed.dat):

d1: DISTANCE ATOMS=15,104 RESTRAINT ARG=d1 AT=0.5 KAPPA=1000

Then run GROMACS with:

gmx mdrun -plumed plumed.dat

✅ This is the recommended method if your atoms are in different molecules and cannot be merged.

⚠️ A Note on Type 10 Restraints

Setting type=10 in distance_restraints still does not allow inter-molecular restraints unless atoms are in the same moleculetype. The type only changes how the potential is calculated — it doesn't bypass scope limitations.

✅ Summary

Problem Cause Solution Atom index out of bounds Using global atom index or referencing other molecule Use local indices in correct moleculetype, or merge molecules Intermolecular restraint needed Atoms in different [ moleculetype ] Use Plumed for restraint Using type=10 doesn’t help Type changes potential, not molecule scope Still must follow topology rules or use external tools