Fix bond/react and prevent reaction within the same molecule

Dear LAMMPS users,

I have been trying to form a crosslinked system using polyacrylic acid molecules (10-mers), i.e., PAA10 and a type of crosslinker molecules using the command fix bond/react. However, I found that the two end groups of the same PAA chain could react and form a bond within the same molecule, instead of forming bonds with other PAA chains, which prevents this molecule from participating in the polymerization process.

I have been trying to fix the problem by defining in the Molecules section of the pre-reaction template that the atoms related to the two reaction sites must be from different molecules (by giving them different molecule IDs 1 and 2) and all atoms in the post-reaction template should have the same molecule ID of 1. It did not seem to prevent the formation of loops. I have also considered adding constraints in the map file, for example, based on distance, but could not think of a way to do it. I was wondering if you could kindly help me with this problem.

I apologize if I missed something or was not doing something correctly. Thank you very much for your help.

the current version of ‘fix bond/react’ has the option to prevent intramolecular reactions. take a look at the ‘molecule’ keyword, and please let us know if you have any further questions

Thanks so much for your help. I am sorry that I missed this part of the documentation.