In present time, computer simulation has become an important instrument in science and research work. Information technologies are developing very quickly and simulation methods are also improved. Modern computers can calculate the processes with millions particles and visualize the structure of materials with details on atomic level. There are many different techniques for simulation. The most considerable and fundamental are Monte-Carlo method, molecular dynamics, phenomenological method, first-principles calculations. The molecular dynamics is one of the most popular methods, because it has several important advantages: it is based on Newton's dynamic equation, which allowing a natural way to describe the evolution of the particle system, consideration of the problem occurs at the atomic level with regard to the matter microstructure, one can consider a system of several hundreds of thousands of atoms