Calculation of thermal conductivity with molecular dynamics is possible but its hectic..with DFT or paid software like Quantam ATK its easy...please go through the papers below it might help you understanding.
https://iopscience.iop.org/article/10.1088/1361-6528/aae98b#:~:text=Previous%20studies%20reported%20that%20graphene,significant%20decrease%20in%20thermal%20conductivity.
Article Molecular dynamics simulations of thermal conductivity betwe...
Article Molecular dynamics simulations of thermal conductivity of ca...
Article Molecular-dynamics simulation of thermal conductivity of sil...
Hello. First of all it is essential to know which software is better for your purpose. I recommend LAMMPS for TC calculation because it has an ability to compute heat conductivity directly. I think this website address can be helpful:
https://lammps.sandia.gov/doc/compute_heat_flux.html#compute-heat-flux-command
You can find installation package and other commands in the website easily.
Good luck.
LAMMPS is using an incorrect formula for thermal conductivity, which only works for pair potentials. Please see many of our recent publications on how to correctly compute this quantity from MD.
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