A multiple time-step method for molecular dynamics simulations of fluids of chain molecules

Swindoll, R.D; Haile, J. M.

doi:10.1016/0021-9991(84)90042-1

Cited by 50 publications

(26 citation statements)

References 8 publications

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“…If the system to be studied has to handle particles with high velocities, algorithms with multiple time steps could be used (Tuckerman et al 1990;Swindoll & Haile 1984;Teleman & Jonsson 1986). Still, if even with these methods the simulation is not practical or does not portray the system accurately, it might be recommended to use an HSDEM program instead of an SSDEM.…”

Section: Particle-particle Interactionmentioning

confidence: 99%

Simulating Asteroid Rubble Piles With a Self-Gravitating Soft-Sphere Distinct Element Method Model

Sánchez¹,

Scheeres²

2011

ApJ

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This paper applies a soft-sphere distinct element method Granular Dynamics code to simulate asteroid regolith and rubble piles. Applications to regolith studies in low gravity are also studied. Then an algorithm to calculate self-gravity is derived and incorporated for full-scale simulations of rubble-pile asteroids using Granular Dynamics techniques. To test its validity, the algorithm's results are compared with the exact direct calculation of the gravitational forces. Further avenues to improve the performance of the algorithm are also discussed.

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Section: Particle-particle Interactionmentioning

confidence: 99%

Simulating Asteroid Rubble Piles With a Self-Gravitating Soft-Sphere Distinct Element Method Model

Sánchez¹,

Scheeres²

2011

ApJ

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“…This difference is then used to improve upon the quasi-separate propagation, without incurring significant additional computational cost. The method of Swindoll and Haile [22] is also more accurate than that of Teleman and Jonsson [21], but it needs higher-order spatial derivatives of the potential. This has to be avoided here, since most of the time is already spent calculating first derivatives.…”

Section: Introductionmentioning

confidence: 98%

Multiple time scale Hartree–Fock molecular dynamics

Hartke

Gibson

Carter

1993

Int J of Quantum Chemistry

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This is the first application of a rigorous, established multiple time-step method to ab initio molecular dynamics. The resulting algorithm is conceptually simple and easy to implement, but very effective. It translates the large mass differences present in ab initio molecular dynamics into substantial savings in computer time while retaining high accuracy. This transforms ab initio molecular dynamics from a desirable but prohibitively expensive possibility into a viable method, at least for short-time phenomena in small systems or for otherwise inaccessibly complicated potential energy surfaces.

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“…51,[72][73][74][75][76][77][78][79] The various available MTS schemes differ in the way they approximate the slowly varying force contribution at each microintegration time step. 79 Common approximations are: (1) to omit it and reintroduce its effect as a trajectory correction at each macrointegration time step (NAPA 67 and RESPA 68, 69 schemes); (2) to include it as a time-independent contribution [80][81][82] and, possibly, reintroduce the effect of its time dependence as a trajectory correction at each macrointegration time step; 69,70 (3) to extrapolate its time dependence based on a Taylor-series expansion 83,84 or some other extrapolation method; [85][86][87] (4) to approximate its time dependence so as to enforce equivalence with the standard Verlet integrator (so-called Verlet equivalence) when all forces are treated as slowly varying forces (Verlet-II 73 and Verlet-X 88 schemes); (5) to omit it and reintroduce it as a force contribution acting only at the beginning and at the end of each macrointegration time step (impulse schemes, such as the Verlet-I scheme 73 and the equivalent but more general r-RESPA scheme, 51,[74][75][76]89 or the mollified-impulse MOLLY scheme [90][91][92] ). The latter impulse-based MTS schemes are attractive because the corresponding integrators are both time-reversible and symplectic (and generally second-order accurate), which is generally not the case for the other MTS methods.…”

Section: Introductionmentioning

confidence: 99%

A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations

Kräutler

Hünenberger

2006

J Comput Chem

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A new algorithm is introduced to perform the multiple time step integration of the equations of motion for a molecular system, based on the splitting of the nonbonded interactions into a series of distance classes. The interactions between particle pairs in successive classes are updated at a progressively decreasing frequency. Unlike previous multiple time-stepping schemes relying on distance classes, the present algorithm sorts interacting particle pairs by their next update times rather than by their update frequencies. For this reason, the proposed scheme is extremely flexible with respect to the number of classes that can be employed (up to hundred or more) and the distance dependence of the relative time step size (arbitrary integer function of the distance). It can also easily be adapted to classes defined based on a criterion other than the interparticle distance (e.g., interaction magnitude). Different variants of the algorithm are tested in terms of accuracy and efficiency for simulations of a pure water system (6167 molecules) under truncated-octahedral periodic boundary conditions, and compared to the twin-range method standardly used with GROMOS96 (short- and long-range cutoff distances of 0.8 and 1.4 nm, pair list and intermediate-range interactions updated every five steps). In particular, multiple time-stepping schemes with an accuracy comparable to that of the twin-range method can be designed, that permit to increase the effective (long-range) cutoff distance from 1.4 to 3.0 nm with a performance loss of only about a factor 2. This result is quite encouraging, considering the benefits of doubling the cutoff radius in the context of (bio-)molecular simulations.

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A multiple time-step method for molecular dynamics simulations of fluids of chain molecules

Cited by 50 publications

References 8 publications

Simulating Asteroid Rubble Piles With a Self-Gravitating Soft-Sphere Distinct Element Method Model

Simulating Asteroid Rubble Piles With a Self-Gravitating Soft-Sphere Distinct Element Method Model

Multiple time scale Hartree–Fock molecular dynamics

A multiple time step algorithm compatible with a large number of distance classes and an arbitrary distance dependence of the time step size for the fast evaluation of nonbonded interactions in molecular simulations

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