You may read this publication by Lervik et al. :

Article Heat transfer in protein–water interfaces

Dear,

As per my understanding, Its a bit challenging as classical methods doesnot explicitly handle the quantum effects. Still, there are various atempts have been made in past and the field is open.

I have copied some lines from one of the paper. It might be helpful to you....

A natural question that arises as a result of this work regards the existence of a reliable simulation method for computing thermal conductivities in solids below the Debye temperature. Such a method should be able, if one considers the usual formula of Eq. (6), to predict correctly normal mode heat capacities and lifetimes. At present, it appears that no method based on MD has the ability to achieve both tasks; classical MD fails on both aspects, while the use of a quantum thermostat results in a strong underestimation of the lifetimes. Neither ad hoc rescaling of temperatures nor the use of classical phonon lifetimes within a BTE scheme offers any guarantee in terms of reliability or accuracy, although they may work reasonably well for specific systems. For simple crystal systems, a satisfactory alternative is the use of lattice dynamics techniques for computing the phonon lifetimes, based on quantum perturbation theory and using the cubic term in the expansion of the potential energy [8,33]. Such a method is, however, computationally intensive and tedious. More importantly, it does not seem to be applicable to disordered systems or even to crystals with complex unit cells. Therefore, the calculation of heat conductivity from numerical simulations in such systems at low temperature remains an open challenge.

Article Thermal conductivity decomposition and analysis using molecu...

http://ilm-perso.univ-lyon1.fr/~drodney/dr_articles/2014_PRB%5BBedoya_Barrat_Rodney_ThermalConductivity%5D.pdf

Hope it may help you in some or other way.

You can calculate thermal conductivity using Lammps using difference in heat flux (Green-Kubo method.) Please check the manual https://lammps.sandia.gov/doc/compute_heat_flux.html for documentation

Thank you everyone for your informative reply