One of the current high priority safety issues of nuclear power plants is atmosphere stratification in the containments. It requires extensive experimental and numerical investigations. Numerical investigation of stratification using lumped-parameter codes is complicated due to inherent limitations of the codes. These limitations have to be taken into account in developing nodalisation of the containments. The paper presents M5 experiment simulations using lumped parameter code COCOSYS. Experiment M5 was performed in the MISTRA test facility in the frames of FP-6 project SARNET (Severe Accident Research Network). Obtained results are presented in the context of evaluation of the lumped-parameter code COCOSYS capabilities to model the formation of stratified atmosphere and to give recommendations for the development of nodalisations in similar cases using any lumped-parameter code. The paper describes the MISTRA test facility and the performed experiment M5, the gas flow model of the COCOSYS code, the developed nodalisations, and the obtained results. The performed analysis showed that detailed vertical nodalisation and special treatment of injected gas flow is required for simulation of gas mixing phenomena.