The virial stress tensor-based instantaneous heat flux, which is used by LAMMPS, is only valid for the small subset of simulations that contain only pairwise interactions. For systems that contain many-body interactions using 3- or 4-body potentials, a more complete derivation is required. We have created a software patch to LAMMPS that implements the correct heat flux calculation approach for 3- and 4-body potentials, based on the derivation by Torii et al. ( J. Chem. Phys. 2008 , 128 , 044504 ) Using two example systems, the error in the uncorrected code for many-body potential heat flux is shown to be significant and reaches nearly 100% of the many-body potential heat flux for the systems we studied; hence, the error of the total heat flux calculation is proportional to the fraction of the total heat flux transferred through the many-body potentials. This error may have consequences for thermal conductivities calculated using the Green-Kubo method or any NEMD method that uses the instantaneous heat flux. We recommend that all researchers using LAMMPS for heat flux calculations where significant heat is transferred via the many-body potentials adopt the corrected code.