The paper contains a description of a multiscale algorithm based on the boundary element method (BEM) coupled with a discrete atomistic model. The atomic model uses empirical pair-wise potentials to describe interactions between atoms. The Newton-Raphson method is applied to solve a nanoscale model. The continuum domain is modelled by using BEM. The application of BEM reduces the total number of degrees of freedom in the multiscale model. Some numerical results of simulations at the nanoscale are shown to examine the presented algorithm.