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Musculoskeletal model-based simulation can be a powerful tool in the evaluation of exoskeletons. An ideal exoskeleton model, perfectly aligned with the human joint axes, can be used to co-simulate the human and exoskeleton dynamics. However, human-exoskeleton joint misalignment is commonly observed during the use of an exoskeleton. Using misaligned motion data in the combined human-exoskeleton model can lead to unrealistic results. In this work, we present a new method to align human-exoskeleton models. This was achieved by introducing dummy segments that ensured kinetic alignment between the human and exoskeleton joints without altering the misaligned kinematics. The method was applied on an active lower-limb exoskeleton that assists the elderly in stair negotiation. In a pilot study, motion data of a single subject testing the exoskeleton in stair ascent were recorded using an optical marker-based system. Measured ground reaction force and exoskeleton assistive force were used as inputs in the human-exoskeleton model. The outputs from the model with the dummy segments were compared to those from a model with kinematic constraints and a reference model where the external forces were applied directly to the human model. The results of the knee compression force, knee flexion moment, and activation of vastus lateralis showed good agreement between the dummy segments and reference models. The use of the dummy segments allows the study of aligned kinetics and misaligned kinematics from the same model. The method will be used in a future study to evaluate the exoskeleton with more subjects.