Vacuum molecular dynamics simulation energy calculations

Once the boundary conditions have been implemented, the calculation of solution molecular dynamics proceeds in essentially the same manner as do vacuum calculations. While the total energy and volume in a microcanonical ensemble calculation remain constant, the temperature and pressure need not remain fixed. A variant of the periodic boundary condition calculation method keeps the system pressure constant by adjusting the box length of the primary box at each step by the amount necessary to keep the pressure calculated from the system second virial at a fixed value (46). Such a procedure may be necessary in simulations of processes which involve large volume changes or fluctuations. Techniques are also available, by coupling the system to a Brownian heat bath, for performing simulations directly in the canonical, or constant T,N, and V, ensemble (2,46). 

---