Suppose, a polymer has 3 monomers in its chain:
$$\ce{A1-A2-A3}$$
When calculating total LJ potential, do I need to calculate like this: $$E(r_{12})+E(r_{23})+E(r_{31})$$
Or, do I calculate: $$E(r_{12})+E(r_{23})$$
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1 Answer
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You'll want to add up all interactions that you can, up to some appropriately chosen cutoff distance. Choose the VDW cutoff such that the total energy doesn't change much if you further increase this number.
In your case, it's likely you'll want to include all three interactions, unless the monomers themselves are very large such that $E(r_{31})$ is very small relative to the other two terms.
