This is a description of some methods available to study dynamical and chemical stability, not limited to MD:
Dynamical stability. The question here is: given a compound in a particular structure, is this structure dynamically stable or is there a lower-energy structure that can be accessed without jumping over an energy barrier? From a potential energy surface (PES) point of view, the question is: is this structure at a local minimum of the PES, or is it at a saddle point? The most straight-forward way of answering this question is to perform a phonon calculation. If all phonon frequencies are real, then the system is dynamically stable (at a local minimum), but if there are some imaginary frequencies, then the system may be dynamically unstable (at a saddle point). So my immediate suggestion would be to do a phonon calculation (which is also much cheaper than an MD simulation). If all frequencies are real, then you are done, the structure is dynamically stable. If you encouter imaginary frequencies, then the structure may or may not be dynamically stable. The structure definitely sits at a saddle point of the PES, but entropic contributions may help stabilize it at finite temperature (you are looking at the free energy surface rather than at the PES). A well-known example of this latter case is that of perovskites, which undergo a series of temperature-induced structural phase transitions. In this case, phonons are of no use (the relevant terms are anharmonic), and MD may come in handy. My suggestion would then be to start with the lower energy structure that the imaginary phonons take you to, and then run and MD simulation to see if the structure "symmetrizes" from the local minimum to the saddle point.
Chemical stability. The question here is: given a compound with a particular stoichiometry, will is decompose into other compounds? MD is not really a viable way to answer it in general; instead, you probably want to go down the route of structure prediction. What you would do is to generate multiple candidate structures at different stoichiometries, and then construct a Hull diagram to investigate if your structure will stay put or decompose. MD can simply not access the long time scales that are necessary to see something like a phase decomposition.