How to exempt bond creation within single monomer using bond/create command

LAMMPS LAMMPS General Discussion
1

Hello,

I am simulating the polymerization of EDOT monomers using LAMMPS’s fix bond/create command. Polymerization should occur between one Alpha Carbon of one monomer and another alpha Carbon of another monomer. But the problem is that each monomer has two unbonded alpha Carbons. So, the bond creation was done within each monomer rather than between different monomers simply because the two alpha Carbons of each monomer satisfy the bond distance criterion. Can you please suggest to me how to exempt bond creation from two identical atoms (same atom type) within each monomer from bonding?

2

Fix bond/create is rather simple-minded and thus not applicable to complex situations beyond what is explained in its documentation. Please have a look at fix bond/react instead for a much more sophisticated command.

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