This chapter is dedicated to classical problems of thermal instability like the Bénard-Rayleigh problem occurring in the Earth atmosphere, which can be simulated in the laboratory in a square cavity filled with a fluid and bounded by parallel plates. The problem of the thermal instability is treated at first from the classical viewpoint based on the linear convection theory, deriving from the conservation equations for mass, momentum, and energy linear dimensionless equations which can then be solved in case of appropriate boundary conditions (mainly free bounding surfaces or rigid bounding surfaces). The analytical background presented relies upon the treatment given in Koschmieder (1993) and Chandrasekhar (1961). Applications of the molecular dynamics to the Bénard-Rayleigh are preceded by information about the computer program SQUARE CAVITY built for the purpose. Applications of this code are then made for the classical Bénard-Rayleigh problem with rigid surfaces and for a problem of concentric surfaces in a 2D representation. A section is then dedicated to a two-dimensional flow around a circular obstacle at high Reynolds number. The chapter closes with a simulation of thermal creep with a fluid initially at rest, but bounded by surfaces displaying a temperature gradient. The chapter does not present any novelty from the theoretical viewpoint but it intends to offer young scientist a help by discussing typical classical examples.