Thermal transport in a water–Cu nanocolloid system was investigated using equilibrium molecular dynamics. A systematic analysis of the Green–Kubo calculations is presented to clarify the effect of simulation parameters. Several sources of error were identified and quantified for the thermal conductivity estimations, and the effect of the base fluid potential was investigated. Simulations were carried out with a single copper particle for different diameters and water potentials, and thermal enhancements exceeding both theoretical and experimental results were observed in parallel with some other studies in the literature. The anomalous Green–Kubo thermal enhancement results could be explained by the interfacial dynamics and the neglect of calibrating the interaction potential to satisfy the physically-observed energy flow at the interface.