The study of molecular properties is essential to understand the origin of thermodynamic stability of the confined liquid. Molecular dynamics (MD) simulations are carried out to study the pressure driven water flow through carbon nanotubes. Present study shows how the selection of thermostat affects the physical behavior of confined fluid in nanoscale channels and its consequences. We have used three different thermostats - Nosé Hoover, Langevin, and Berendsen, to study the influence of thermostat selection on the reorientation and power spectra of confined fluids. The determination of these properties will help us to investigate the intramolecular dynamics and the motion of the confined molecules. The results indicate that care should be employed while performing MD computations of confined fluids in carbon nanotubes, thermostating the confined fluid can lead to significant unphysical behavior of the fluid, which may lead to wrong interpretations. © 2013 Elsevier B.V.