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Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case, however, that the interparticle forces drive motion on many time scales, and the efficiency of a calculation is limited by the choice of time step, which must be sufficiently small that the fastest force components are accurately integrated. Multiple time-stepping algorithms partially alleviate this inefficiency by assigning to each time scale an appropriately chosen step-size. However, such approaches are limited by resonance phenomena, wherein motion on the fastest time scales limits the step sizes associated with slower time scales. In atomistic models of biomolecular systems, for example, resonances limit the largest time step to around 5-6 fs. In this paper, we introduce a set of stochastic isokinetic equations of motion that are shown to be rigorously ergodic and that can be integrated using a multiple time-stepping algorithm that can be easily implemented in existing molecular dynamics codes. The technique is applied to a simple, illustrative problem and then to a more realistic system, namely, a flexible water model. Using this approach outer time steps as large as 100 fs are shown to be possible.
|Publication status||Published - 2013|
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- 1 Finished
Science and Innovation: Numerical Algorithms and Intelligent Software for the Evolving HPC Platform
1/08/09 → 31/07/14