The average specific volume of the model poly(3-aminopropyl methyl siloxane) as a function of temperature near the glass transition was computed from molecular dynamics simulations. The glass transition temperature was defined as the slop intersection around 210 K, a value similar to that of the experimental result. Globular polymer shaped chains were observed where the chain is closed upon itself. Three amino groups of amino propylene chains were located in the center and the rest of the amino groups were situated outside the main chain. The glass transition temperature of this low molecular weight polymer strongly depends on the binding energies between chains. The intersection of binding energy slopes defines a temperature of 213 K near the glass transition temperature. The most important contributions to the glass transition changes were the electrostatic binding contributions. The Van der Waals contributions in the volume changes were less important. The chain mobility was evaluated by the transition between angles for the states trans, g(+) and g(-). The glass transition temperature observed experimentally, 208 +/- 2 K, is due to cooperative movements of two different torsion angles, (O-Si) and (Si-C) of the main chain and the lateral chain, respectively, and its rotational mobility. Self-diffusion constant variation for all polymer atoms with the temperature is a probe that the polymer chain cooperative movement had started at temperatures around the glass transition temperature.