We study thermal transport properties by conduction using molecular dynamics simulations. In our approach, two portions are delimited and heated at two different temperatures before the approach-to-equilibrium in the whole structure is monitored. The observed decay of the temperature difference is interpreted and used to extract thermal properties of systems ranging from bulk materials, interfaces and nanoconstrictions. First we study the case of bulk. The numerical results are compared to the corresponding solution of the heat equation and a relation is found between the decay time and the bulk conductivity. The method is applied to bulk silicon modeled with Tersoff potential. Systems longer than one micrometer are studied thanks to the reduced computational cost of the method. The bulk conductivity is extrapolated and an excellent agreement with previous calculations is obtained. The approach is used afterwards to predict the thermal conductivity of germanium and alpha-quartz. The method is also applied to the case of different materials in the two heated portions. The lump capacitance assumption is extended to extract the boundary conductance. The application is made on the crystalline silicon/amorphous silicon or silica interface. The method is shown to be sensitive enough to enable the determination of the low interface resistance despite the presence of a poor conductor on one side of the interface. Finnaly, current investigation dedicated to nanoconstrictions are presented. These multiple applications illustrate that the AEMD method is ideally suited for studying atomic-scale systems including complex features, such as nanostructures, disordered materials and lightly to strongly resistive interfaces