I’m trying to use fix bond/react to create a polymer network. The crosslinker has three reaction sites, all with the same topology, and the monomer has two active sites, both with the same topology. The simulation runs successfully but no reactive events occur despite the atoms that I intended to set with BondingIDs being within the Rmin - Rmax range. Based on dumping the bond_react_MASTER_group, I think the dynamic group is never populated. My guess is that I’m not defining the molecule templates correctly but I haven’t been able to figure out what is wrong. The templates both contain entire molecules and as far as I can tell the topology in the templates matches that of the initial data file. Could someone please advise on what my error might be or where I should look to debug? As a new user I can’t upload attachments, but hopefully I can add them once the topic is created.
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Including the entire molecule in the reaction templates will not work for polymerization, because bond/react will look for matches with the entire molecule, but that topology will change after the first link (essentially each monomer could only form one crosslink, and it looks like your two unreacted monomers happen to be too separated in their initial configuration). Instead, you should include only as many atoms as needed in the templates, in your case atoms within three bonds of reacting atoms. Atoms in the pre-reaction template that would connect to the rest of a polymer chain should be labeled ‘edge’ atoms in the map file (see /examples/USER/reaction). Using these minimal templates will also avoid issues in parallel if you need to scale up to large simulations.