Stochastic Dynamics Simulations of Barrier Crossing in Solution

Stochastic Dynamics Simulations of Barrier Crossing in Solution 

Activated processes in solution, such as conformational transitions for biomolecules that are fully exposed to solvent, can be treated by stochastic dynamic simulation methods (see Chapt. I V.D). Their use requires a knowledge of the solvent contribution to the potential of mean force. Also, the system must be small enough so that the simulation times can be extended to the nanosecond or microsecond range required to adequately sample the statistically rare events involved in activated processes. Alternatively, activated dynamics techniques can be used with a stochastic dynamics simulation.307,335 

As a model for such surface sidechain transitions, we consider here the 

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