  We propose a way to properly interpret the apparent thermal conductivity
obtained for finite systems using equilibrium molecular dynamics simulations
(EMD) with fixed or open boundary conditions in the transport direction. In
such systems the heat current autocorrelation function develops negative values
after a correlation time which is proportional to the length of the simulation
cell in the transport direction. Accordingly, the running thermal conductivity
develops a maximum value at the same correlation time and eventually decays to
zero. By comparing EMD with nonequilibrium molecular dynamics (NEMD)
simulations, we conclude that the maximum thermal conductivity from EMD in a
system with domain length 2L is equal to the thermal conductivity from NEMD in
a system with domain length L. This facilitates the use of nonperiodic-boundary
EMD for thermal transport in finite samples in close correspondence to NEMD.
