Multiple time-step methods in molecular dynamics

Streett, William B.; Tildesley, Dominic J.; Saville, G.

doi:10.1080/00268977800100471

Cited by 203 publications

(84 citation statements)

References 16 publications

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“…Multiple time scale methods can be used to exploit this separation in time scales by updating the slow interactions less frequently than the fast interactions, in principle, allowing significant computational savings to be achieved. [1][2][3][4] However, the maximum outer time step which can be obtained is in practice limited by the resonance between the slow and fast modes. 5,6 This results in energy building up in the high frequency modes, raising the temperature of the system and leading to unstable trajectories and incorrect sampling.…”

Section: Introductionmentioning

confidence: 99%

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Morrone

Markland

Ceriotti

et al. 2011

The Journal of Chemical Physics

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Multiple time scale molecular dynamics enhances computational efficiency by updating slow motions less frequently than fast motions. However, in practice, the largest outer time step possible is limited not by the physical forces but by resonances between the fast and slow modes. In this paper we show that this problem can be alleviated by using a simple colored noise thermostatting scheme which selectively targets the high frequency modes in the system. For two sample problems, flexible water and solvated alanine dipeptide, we demonstrate that this allows the use of large outer time steps while still obtaining accurate sampling and minimizing the perturbation of the dynamics. Furthermore, this approach is shown to be comparable to constraining fast motions, thus providing an alternative to molecular dynamics with constraints.

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Section: Introductionmentioning

confidence: 99%

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Morrone

Markland

Ceriotti

et al. 2011

The Journal of Chemical Physics

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show abstract

“…However, recent improvements to the spatial decomposition have enabled good scaling behavior down to a few hundred atoms per processor as well as about 10% improvement in performance for the spatial decomposition for some systems [59]. Another group of researchers implemented a version of the decomposition which employs a multiple time-step method [60] and three-body interactions [14,61,62] and then applied to several problems in porous silica [63,64].…”

Section: Spatial Parallel Molecular Dvnamics Algorithmmentioning

confidence: 99%

Parallel atomistic simulations

Heffelfinger

2000

Computer Physics Communications

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“…In spite of the rarity of interactions at low density, the inherent time step in SMD simulations cannot be increased beyond some small threshold without loss of stability and accuracy of trajectories, since there is nearly always a small fraction of particles interacting at any given time. Several adaptive integration methods exist, typically based on either separating rapidly and slowly-varying components of the potential in a multiple time step approach [3], or on time re-parametrization of the Hamiltonian equations to a new system that is integrated with a fixed step size [4]. Both methods have inherent drawbacks making them unsuitable for arbitrary potentials.…”

Section: Introductionmentioning

confidence: 99%

Event-driven dynamics of rigid bodies interacting via discretized potentials

Zon

Schofield

2008

The Journal of Chemical Physics

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A framework for performing event-driven, adaptive time step simulations of systems of rigid bodies interacting under stepped or terraced potentials in which the potential energy is only allowed to have discrete values is outlined. The scheme is based on a discretization of an underlying continuous potential that effectively determines the times at which interaction energies change. As in most event-driven approaches, the method consists of specifying a means of computing the free motion, evaluating the times at which interactions occur, and determining the consequences of interactions on subsequent motion for the terraced-potential. The latter two aspects are shown to be simply expressible in terms of the underlying smooth potential. Within this context, algorithms for computing the times of interaction events and carrying out efficient event-driven simulations are discussed. The method is illustrated on system composed of rigid rods in which the constituents interact via a terraced potential that depends on the relative orientations of the rods.

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Multiple time-step methods in molecular dynamics

Cited by 203 publications

References 16 publications

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Efficient multiple time scale molecular dynamics: Using colored noise thermostats to stabilize resonances

Parallel atomistic simulations

Event-driven dynamics of rigid bodies interacting via discretized potentials

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