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The numerical global Upper Atmosphere Model (UAM) has been used for studying the lower thermosphere and ionosphere behaviour during a strong magnetic storm of March 31, 2001. A comparison of the calculation results with the Millstone Hill IS radar data obtained during this magnetic storm has been carried out. A satisfactory agreement between the measured and calculated ion temperatures, electron and ion drift velocities has been obtained. The calculated electric field variation is similar to the observed one but is twice less in magnitude. As to the neutral horizontal wind velocities, there is a large difference between the calculated values and data obtained by the Millstone Hill IS radar, down to the different signs of the wind components. This difference can be bound up to distinctions in the frequencies of the ion-neutral collisions dependent on the neutral atmosphere parameters and the ion composition, and in the electric fields measured at Millstone Hill and theoretically calculated by the UAM. The reasons of the discrepancy of the thermospheric winds simulated by the UAM and calculated at Millstone Hill have been examined. The results of this examination show that the Millstone Hill wind results are very sensitive to the measured electric field values especially when the last are so large as they were in the case, and therefore even a moderate difference between the calculated and observed electric fields may cause a significant discrepancy of the thermospheric winds simulated by the UAM and calculated at Millstone Hill.