Projects per year
Abstract
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 coarsegrained 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 timestepping algorithms partially alleviate this inefficiency by assigning to each time scale an appropriately chosen stepsize. 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 56 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 timestepping 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.
Original language  English 

Pages (fromto)  35793594 
Journal  Molecular Physics 
Volume  111 
Issue number  2223 
DOIs  
Publication status  Published  2013 
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Projects
 1 Finished

Science and Innovation: Numerical Algorithms and Intelligent Software for the Evolving HPC Platform
1/08/09 → 31/07/14
Project: Research