Large deck openings of ultra large container ships reduce their torsional stiffness considerably and hydroelastic analysis for reliable structural design becomes an imperative. In the early design stage the beam model coupled with 3D hydrodynamic model is a rational choice. The modal superposition method is ordinary used for solving this complex problem. The advanced thin-walled girder theory, with shear influence on both bending and torsion, is applied for calculation of dry natural modes. It is shown that relatively short engine room structure of large container ships behaves as the open hold structure with increased torsional stiffness due to deck effect. Warping discontinuity at the joint of the closed and open segments is compensated by induced distortion. The effective torsional stiffness parameters based on an energy balance approach are determined. Estimation of distortion of transverse bulkheads, as a result of torsion and warping, is given. The procedure is illustrated in the case of a ship-like pontoon and checked by 3D FEM analysis. The obtained results encourage incorporation of the modified beam model of the short engine room structure in general beam model of ship hull for the need of hydroelastic analysis, where only the first few natural modes are of interest.