Construction of the molecular model

1 Construction of the molecular model For non-charged, monoatomic systems we assume pairwise additivity of interactions. We then write for the potential energy function 

The pairwise interaction potential can be described by a Lennard-Jones potential. 

In Table 14.1, interaction parameters are shown for some atoms (see the book by Allen and Tildesley for parameters of more atoms). 

For unlike atoms, the Lorentz-Berthelot combining rules are used to determine the Lennard-Jones parameters. These rules are as follows  

For molecular species we need more terms to model the internal degrees of freedom and their interactions. Typically the additional energy terms are associated with covalent bonds, bond angles, and dihedral angles. We consider systems with M molecules with Nm atoms each for a total of A = M x Nm atoms in the system. 

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