Although modern buildings are using increasingly sophisticated energy management and control systems that have tremendous control and monitoring capabilities, building systems routinely fail to perform as designed. More advanced building control, operation, and automated fault detection and diagnosis (AFDD) technologies are needed to achieve the goal of net-zero energy commercial buildings. Much effort has been devoted to develop such technologies for primary heating ventilating and air conditioning (HVAC) systems, and some secondary systems. However, secondary systems, such as fan coil units and dual duct systems, although widely used in commercial, industrial, and multifamily residential buildings, have received very little attention. This research study aims at developing tools that could provide simulation capabilities to develop and evaluate advanced control, operation, and AFDD technologies for these less studied secondary systems. In this study, HVACSIM+ is selected as the simulation environment. Besides developing dynamic models for the above-mentioned secondary systems, two other issues related to the HVACSIM+ environment are also investigated. One issue is the nonlinear equation solver used in HVACSIM+ (Powell's Hybrid method in subroutine SNSQ). It has been found from several previous research projects (ASRHAE RP 825 and 1312) that SNSQ is especially unstable at the beginning of a simulation and sometimes unable to converge to a solution. Another issue is related to the zone model in the HVACSIM+ library of components. Dynamic simulation of secondary HVAC systems unavoidably requires an interacting zone model which is systematically and dynamically interacting with building surrounding. Therefore, the accuracy and reliability of the building zone model affects operational data generated by the developed dynamic tool to predict HVAC secondary systems function. The available model does not simulate the impact of direct solar radiation that enters a zone through glazing and the study of zone model is conducted in this direction to modify the existing zone model. In this research project, the following tasks are completed and summarized in this report: 1. Develop dynamic simulation models in the HVACSIM+ environment for common fan coil unit and dual duct system configurations. The developed simulation models are able to produce both fault-free and faulty operational data under a wide variety of faults and severity levels for advanced control, operation, and AFDD technology development and evaluation purposes; 2. Develop a model structure, which includes the grouping of blocks and superblocks, treatment of state variables, initial and boundary conditions, and selection of equation solver, that can simulate a dual duct system efficiently with satisfactory stability; 3. Design and conduct a comprehensive and systematic validation procedure using collected experimental data to validate the developed simulation models under both fault-free and faulty operational conditions; 4. Conduct a numerical study to compare two solution techniques: Powell's Hybrid (PH) and Levenberg-Marquardt (LM) in terms of their robustness and accuracy. 5. Modification of the thermal state of the existing building zone model in HVACSIM+ library of component. This component is revised to consider the transmitted heat through glazing as a heat source for transient building zone load prediction In this report, literature, including existing HVAC dynamic modeling environment and models, HVAC model validation methodologies, and fault modeling and validation methodologies, are reviewed. The overall methodologies used for fault free and fault model development and validation are introduced. Detailed model development and validation results for the two secondary systems, i.e., fan coil unit and dual duct system are summarized. Experimental data mostly from the Iowa Energy Center Energy Resource Station are used to validate the models developed in this project. Satisfactory model performance in both fault free and fault simulation studies is observed for all studied systems.