The outstanding obstacle to estimate vibration level is that the precise damping of fluid and structure can not be estimated because the mechanism of the damping has not been explicated. Recently, the damping matrix based on dissipation energy caused by fluid viscosity is obtained, and the damping matrix is expressed more rationally by introducing modulus of velocity distribution β _w as a parameter to estimate the influence of the water depth. We developed a method to experimentally obtain β _w in the shallow water. But the method is not applicable to the deep water because of approximation in the shallow water. In this paper, we propose a method, which can be applied to the deep water, and obtain β _w by using the method. It is known that β _w in the deep water equals 1.0 , by comparing experiment with theory of dissipation energy at peak frequency of 2-node vibratioe. But, in this paper, β _w is obtained by considering not only a peak but also whole area of the frequency and moreover by using curve fit algorithm through not only one peak but also the whole peak. Concretely, authors incorporate reduced added matrixes into transfer function by means of modal structural modification analysis, and formulate the partial differential iteration method by using the transfer function The formulation and the results are described