[lammps-users] Question about Fix bond/create

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1

Dear LAMMPS Community:

I am going to use the Fix bond/create to create bonds between atom type_1 and atom type_2. Type_1 is in molecule_1 (say, carbon in methylene group) and type_2 is in molecule_2 (say, carbon in benzene). The goal is to link two molecules of type molecule_2 together via creating two covalent bonds between atom types type_2 and type_1 (like this {type_2 ---- type_1 ----- type_2}). The question is how to avoid creating such bond in an individual molecule? For example, how can I avoid the creation of bonds between two carbon atoms as type_2 in one single benzene molecule and a carbon atom as type_1 in methylene group?

Any help would be greatly appreciated.

Farshad

2

To impose this restriction in the general case, would require
some additional option/code be added to fix bond/create.
We haven't done this yet, b/c there is nothing in the physics
of bond/creation that should prohibit a bond being created
between 2 atoms in the same molecule, e.g. at opposite
ends of a long polymer chain. Put another way, how would
those 2 atoms "know" they are in the same molecule and
thus should not form a bond?

If your molecules are small, they likely won't create self-bonds.
Or if you have 2 types of molecules in your system you could
use different types for each molecule and thus the itype/jtype
check would prohibit it.

Steve