The model that we have made to simulate the structure of Ni64B36 is taken as the primary configuration. This configuration is then subjected to relaxation under the free boundary, the confined boundary, the periodic boundary and the quasi-dynamical equilibrium boundary through the Morse potential. The energy minimisation method used here is different from that usually taken by other authors in some respects. By comparing and analysing the change of some structure parameters in relaxation, the influence of each kind of boundary on the structure of the model is discussed.