Liquid water models Hamiltonian systems

In Section VII we conclude our results and discuss several issues arising from our proposals. We revisit our original motivation—that is, to find a simple model, in the sense of dynamical systems, that captures several common aspects of slow dynamics in liquid water, or more generally supercooled liquids or glasses. Our attempt is to make clear the relation and compatibility between the potential energy landscape picture and phase space theories in the Hamiltonian dynamics. Importance of heterogeneity of the system is discussed in several respects. Unclarified and unsolved points that still remain but should be considered as crucial issues in slow dynamics in molecular systems are listed. 

We may list differences between the liquid water system and the FPU model the latter will be examined in the next section as a representative system in the study of many-dimensional Hamiltonian systems. The most important difference would be that the FPU model describes a lattice vibration around an equilibrium point and the potential energy function possesses a single minimum, whereas there are infinitely many local potential minima and the potential energy landscape generally becomes ragged in the case of the liquid water system. The reason why the character of the potential landscape could be so important is that the raggedness is considered as an origin of slow motions in liquid water or supercooled liquids. 

In the previous section, we have shown that switching the picture from the nearly integrable Hamiltonian to the Hamiltonian with internal structures may make it possible to solve several controversial issues listed in Section IV. In this section we shall examine the validity of an alternative scenario by reconsidering the analyses done in MD simulations of liquid water. As mentioned in Section III, since a water molecule is modeled by a rigid rotor, and has both translational and rotational degrees of freedom. So, the equation of motion involves the Euler equation for the rigid body, coupled with ordinary Hamiltonian equations describing the translational motions. The precise Hamiltonian is therefore different from that of the Hamiltonian in Eq. (1), but they are common in that the systems have internal structures, and the separation of the time scale between subsystems appears if system parameters are appropriately set. 

Molecular level computer simulations based on molecular dynamics and Monte Carlo methods have become widely used techniques in the study and modeling of aqueous systems. These simulations of water involve a few hundred to a few thousand water molecules at liquid density. Because one can form statistical mechanical averages with arbitrary precision from the generated coordinates, it is possible to calculate an exact answer. The value of a given simulation depends on the potential functions contained in the Hamiltonian for the model. The potential describing the interaction between water molecules is thus an essential component of all molecular level models of aqueous systems. 

The QM/MM Hamiltonian can be used to cany out Molecular Dynamics simulations of a complex system. In the case of liquid interfaces, the simulation box contains the solute and solvent molecules and one must apply appropriate periodic boundary conditions. Typically, for air-water interface simulations, we use a cubic box with periodic boundary conditions in the X and Y directions, whereas for liquid/liquid interfaces, we use a rectangle cuboid interface with periodic boundary conditions in the three directions. An example of simulation box for a liquid-liquid interface is illustrated in Fig. 11.1. The solute s wave function is computed on the fly at each time step of the simulation using the terms in the whole Hamiltonian that explicitly depend on the solute s electronic coordinates (the Born-Oppenheimer approximation is assumed in this model). To accelerate the convergence of the wavefunction calculation, the initial guess in the SCF iterative procedure is taken from the previous step in the simulation, or better, using an extrapolated density matrix from the last three or four steps [39]. The forces acting on QM nuclei and on MM centers are evaluated analytically, and the classical equations of motion are solved to obtain a set of new atomic positions and velocities. 

---