1-2, 1-3, and 1-4 Neighbors in a LAMMPS Simulation


I’m running a LAMMPS simulation of a polydimethylsiloxane (PDMS) polymer. In the output log file, I see the entries ‘4 = max # of 1-2 neighbors’, ‘6 = max # of 1-3 neighbors’, and ‘8 = max # of 1-4 neighbors’. I’m not sure what these 1-2, 1-3, and 1-4 neighbors mean, or how to interpret these maximum counts. Can you explain these concepts to me?

See special_bonds command — LAMMPS documentation . Please note if you are using OPLS-aa (which you might be, simulating a polymer) that the LAMMPS default is special_bonds 0 0 0 (that is, pair and charge interactions are not counted for all 1-2, 1-3 and 1-4 neighbours) while the OPLS-aa published settings correspond to special_bonds 0 0 0.5 (1-4 interactions scaled down by half).

It is a feature of most molecular force fields (i.e. force fields with explicit bonds, angles, and dihedrals), that when there is a bonded interaction, the corresponding non-bonded interaction is excluded. That simplifies the parameterization process massively (e.g. bonded force constants can be directly computed from a vibrational analysis). A 1-2 neighbor is an atom directly bound to a central atom, a 1-3 neighbor is an atom bound to a 1-2 neighbor, and 1-4 neighbors follow the bonds to the 3rd level. This information must be stored with the central atom, so it can encode the special neighbor status into the neighbor list.

For most people those have no immediate meaning. It can be useful when debugging the bond topology for complex molecular systems. The specific numbers reflect how much additional memory is allocated. Those limits come into play, when you want too add more molecules to the system with different requirements (more bonds per atom, or more special neighbors etc.) that will fail and thus the various “extra/*” keywords to read_data need to be used to reserve a sufficient amount of extra space.

For details on special bonds and exclusions, you should read up in a suitable text book on molecular simulations or published journal articles describing the details of specific force fields.

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