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Simulation modeling of computer networks is an effective technique for evaluating the performance of network and data transfer with various internet protocols. In this paper we are focusing on the impact of used transport layer protocol transferred with new internet protocol (IPv6) against network performance, especially network router load and efficiency. Higher values of load or worse efficiency can be a problem in global IPv6 deployment. We propose methodology of traffic measurement based on different stochastic systems. We are able to generate different TCP, UDP and SCTP traffic according to uniform probability distribution for packet inter departure time and packet size. We use a generator that is able to reproduce experiment by using the same seed for random values and we focus on the correlation of packet size, inter departure time to router and communicating nodes load. All experiments were made in pure IPv4 environment and in native IPv6 environment too. We expected that the use of a new protocol lead to higher efficiency of data transfer. By using forward stepwise regression analysis we identify which variables imply the packet transfer time.