Preparing Simulation Data for EGO

To describe a molecule or molecular system, you need to provide a description of the location of the atoms (the atom coordinates) and how they are connected together (the molecule topology). Furthermore, you must also provide force constants for the interactions between atoms which are bonded together, and for interactions between atoms which are not bonded. The former interactions are referred to as the bonded interactions, while the Coulomb and van der Waals interactions are referred to as the non-bonded interactions. Van der Waals $\sigma$ and $\epsilon$ parameters must be specified for interactions between all different types of `like' atoms, and, from these, the parameters for interactions between `different' atoms are derived from the `like' atom parameters using the arithmetic average for sigma and the geometric mean for epsilon:

$${\sigma}_{ij} = \frac{1}{2} ( {\sigma}_{ii} + {\sigma}_{jj} )$$

$${\epsilon}_{ij} = \sqrt{ {\epsilon}_{ii} {\epsilon}_{jj} }$$

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