Thermal transport through nanosystems is central to numerous processes in chemistry, material sciences, electrical and mechanical engineering, with classical molecular dynamics as the key simulation tool. Here we focus on thermal junctions with a molecule bridging two solids that are maintained at different temperatures. The classical steady state heat current in this system can be simulated in different ways, either at the interfaces with the solids, which are represented by thermostats, or between atoms within the conducting molecule. We show that while the latter, intramolecular definition feasibly converges to the correct limit, the molecule-thermostat interface definition is more challenging to converge to the correct result. The problem with the interface definition is demonstrated by simulating heat transport in harmonic and anharmonic one-dimensional chains illustrating unphysical effects such as thermal rectification in harmonic junctions.
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