Nucleic acids Monte Carlo simulation techniques

Intermolecular Interactions by Perturbation Theory Molecular Dynamics and Hybrid Monte Carlo in Systems with Multiple Time Scales and Long-range Forces Reference System Propagator Algorithms Molecular Dynamics Simulations of Nucleic Acids Molecular Dynamics Studies of Lipid Bilayers Molecular Dynamics Techniques and Applications to Proteins Monte Carlo Simulations for Liquid Monte Carlo Simulations for Polymers. 

There are basically two ways to overcome such problems. Firstly, one can thermally excite the system so that it can escape from local minima and continue to search the surrounding conformational space. This is the principle behind molecular dynamics simulations, which generate the trajectory of a molecule in time by numerically integrating Newton s equations of motion. This technique is discussed in another section of the present volume. It is also the principle behind Monte Carlo simulations, which build up a thermodynamic ensemble of molecular conformations based on their Boltzmann probabilities. Application of this approach to nucleic acids is discussed below. 

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