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

On the definitions and simulations of vibrational heat transport in nanojunctions