Simulating Stochastic Dynamics Using Large Time Steps

Abstract

We present a novel approach to investigate the long-time stochastic dynamics of multi-dimensional classical systems, in contact with a heat-bath. When the potential energy landscape is rugged, the kinetics displays a decoupling of short and long time scales and both Molecular Dynamics (MD) or Monte Carlo (MC) simulations are generally inefficient. Using a field theoretic approach, we perform analytically the average over the short-time stochastic fluctuations. This way, we obtain an effective theory, which generates the same long-time dynamics of the original theory, but has a lower time resolution power. Such an approach is used to develop an improved version of the MC algorithm, which is particularly suitable to investigate the dynamics of rare conformational transitions. In the specific case of molecular systems at room temperature, we show that elementary integration time steps used to simulate the effective theory can be chosen a factor ~100 larger than those used in the original theory. Our results are illustrated and tested on a simple system, characterized by a rugged energy landscape.

17 pager, 7 figures

References in corpus (6)

• Coarse Molecular Dynamics of a Peptide Fragment: Free Energy, Kinetics, and Long-Time Dynamics Computations
• Dominant Pathways in Protein Folding
• Quantitative Protein Dynamics from Dominant Folding Pathways
• Stochastic actions for diffusive dynamics: Reweighting, sampling, and minimization
• Dominant Reaction Pathways in High Dimensional Systems
• A geometric framework for phase synchronization in coupled noisy nonlinear systems

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