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This paper introduces a methodology for the longitudinal flight simulation of the ornithopters. An integrative flight simulation framework for the ornithopters is proposed and the fluid-structure-interaction (FSI) was efficiently taken into account. It was realized through the construction of an ornithopter model with flexible wings and applying experimentally validated semi-empirical modified strip theory (MST) to calculate the aerodynamic forces exerted on the flexible flapping-wings. Flexible wings are modeled in the FEA software, ANSYS, and exported to the Multi-body dynamics software, MSC.ADAMS. MSC.ADAMS is used as a backbone of this simulation framework to solve the nonlinear equation of motion of the ornithopter with attached user-defined subroutine containing aerodynamic model for the flexible wings. Longitudinal trimmed level flights of a Magpie sized ornithopter model are simulated in the proposed simulation framework and several trim conditions were found with respect to the various flapping frequency.