Introduction

The total energy ($E_{tot}$) of a system of $M_{mol}$ molecules in classical simulation is usually [5,6] computed as a sum of two contributions, namely

$$E_{tot} = E_{inter} + E_{intra}^{M_{mol}}$$ (1)

where $E_{inter}$ and $E_{intra}^{M_{mol}}$ are the interaction energy among different molecules and the sum of the internal energy of each molecule. In standard FFs, $E_{inter}$ is computed as a sum of pairwise contributions among all the $N_{sites}$ interaction sites used to model the system. In particular,

$$E_{inter} = E_{LJ} + E_{Coul}$$ (2)

where the long-range electrostatic term is

$$E_{Coul} = \sum^{N_{sites}}_{i=1} \sum^{N_{sites}}_{j=1} \frac{q_iq_j}{r_{ij}}$$ (3)

whereas the short range 12-6 Lennard-Jones term is

$$E_{LJ} = \sum^{N_{sites}}_{i=1} \sum^{N_{sites}}_{j=1} 4 \epsilon... ...} {r_{ij} } \bigg )^{12} - \bigg(\frac{ \sigma_{ij} } {r_{ij} } \bigg)^6 \bigg]$$ (4)

where $i$ and $j$ are interaction sites belonging to a pair of different molecules.

The total intramolecular term $E_{intra}^{M_{mol}}$ is the sum of the molecular internal energies ($E^{intra}$) of all the ${M_{mol}}$ molecules composing the system, i.e.

$$E_{intra}^{M_{mol}} = \sum^{M_{mol}}_{K=1} V^{intra}_K$$ (5)

where $V^{intra}_K$ is the internal energy of molecule $K$.
Given a model potential function $V^{intra}_K$, the main goal of the JOYCE program is to find, with respect of reference QM computed data, the best parameters to represent the intramolecular energy for a chosen target molecule $K$, hence parameterizing the intra-molecular term of a QMD-FF..