Techniques for Simulating Reaction Dynamics in Solution

In this section, we wish to give a brief overview of the techniques used in simulating a solution chemical reaction. This discussion will be somewhat self-centered in that we shall focus on the methods we have used, but we shall also give pointers to other methods that can be valuable in particular circumstances. Much of what we discuss here is described in greater detail in Allen and Tildesley.  

The basic outline for performing a classical mechanical simulation is straightforward. One chooses a reaction system (consisting of reactants and products) and a solvent, determines the forces between all the particles, constructs a set of initial conditions (positions and velocities) for the particular physical situation being simulated, and finally runs the molecular dynamics and analyzes the results. There are obviously some further complexities to this simple outline, and we shall cover a few of them in the following. 

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