The most naïve way of specifying, e.g., a protein in a biological model is to specify each of its states explicitly and use each of them as a molecular species in a simulation framework that allows transitions from state to state. For instance, if a protein can be ligand-bound or not, exist in two conformational states (e.g. open or closed) and be located in two possible subcellular areas (e.g. cytosolic or membrane-bound), then the eight possible resulting states can be explicitly enumerated as:
*bound, open, cytosol            
*bound, open, membrane           
*bound, closed, cytosol          
*bound, closed, membrane         
*unbound, open, cytosol          
*unbound, open, membrane         
*unbound, closed, cytosol        
*unbound, closed, membrane
Enumerating all possible states is a lengthy and potentially error-prone process.  For macromolecular complexes that can adopt multiple states, enumerating each state quickly becomes tedious, if not impossible.  Moreover, the addition of a single additional modification or feature to the model of the complex under investigation will double the number of possible states (if the modification is binary), and it will more than double the number of transitions that need to be specified.