FIGURE 3.

Example of an enhanced sampling method consisting on multiple MD simulation replicas at different temperatures (each row). At defined time intervals, which can vary typically from a few to hundreds of ps, the energy of the structures of each replica are evaluated. If the energy of run 1 is lower than that of run 2, or if it is higher but allowed by the Boltzmann factor, the replicas are exchanged, so now the structure from run 1 is simulated at temperature 2, and the structure from run 2 is simulated at temperature 1 (exchange between the top and middle rows). Otherwise, as shown for temperature 3 (lower row), there is no exchange and run 3 continues to be simulated at temperature 3. Exchanges are attempted until all replicas have been run at all temperatures. Structures are then collected as a function of temperature, and data can be analyzed for all temperatures, or only for a particular temperature, of functional or physiological relevance.