Extending Atomistic Time Scale Simulations by Optimization of the Action

Extending Atomistic Time Scale Simulations by Optimization of the Action 

In computational chemistry, molecular dynamics (MD) is the most widely used methodology to study the kinetic and thermodynamic properties of atomic and molecular systems [1-3]. These properties are obtained by solving the microscopic equations of motion for the system under consideration. Due to the short time step that is needed to keep numerical stability, the time scales that can be reached in these simulations are not long, typically on the order of nanosecond to microsecond depending on the complexity of the system. For many systems, like biomolecules, this simulation time is not enough to sample conformational space or to study rare but important events. 

Due to this limitation of straightforward MD algorithms, numerous approaches have been developed. Some of them have aimed to increase the time step size [4-15]. Typical improvements in this multiple steps algorithms are rather modest (one order of magnitude) so they do not provide a satisfactory solution to the timescale problem. 

A different set of methodologies attempt to compute trajectories connecting conformations from the reactant state to conformations of the product state. Tran- 

Department of Chemistry, University of South Florida, Tampa, FI 33620, USA 

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