Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

Schlick, Tamar; Mandziuk, Margaret; Skeel, Robert D.; Srinivas, K.

doi:10.1006/jcph.1998.5879

Cited by 87 publications

(77 citation statements)

References 28 publications

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“…Though the first applications attributed these disturbances to general inaccuracies, they were later recognized as resonance artifacts [10,11]. These artifacts have been analyzed in connection with implicit integration schemes such as implicit midpoint [12] and related integrators [13,14], and with MTS (or force-splitting) schemes [10,11]. Impulse-MTS schemes [6,7] are particularly vulnerable to resonances since relatively large energy pulses are introduced to the governing dynamics equations when the slow forces are evaluated.…”

Section: Mts Approaches and Resonancementioning

confidence: 98%

Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics

Sandu¹,

Schlick²

1999

Journal of Computational Physics

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Section: Mts Approaches and Resonancementioning

confidence: 98%

Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics

Sandu¹,

Schlick²

1999

Journal of Computational Physics

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“…One possible origin of such a peculiar behavior is a resonance problem. 33 Such a phenomenon is considered to be an intrinsic problem in the composition map methods when one deals with the system involving some (especially fast) oscillating mode, using a certain decomposition of the vector field. In fact, the resonance problem is present in the Verlet scheme even in NEV simulations of simple systems.…”

Section: Distributions Of Variablesmentioning

confidence: 99%

“…In fact, the resonance problem is present in the Verlet scheme even in NEV simulations of simple systems. 33,34 The above behavior may be changed by simulation conditions, including the choice of the force field, and by a rearrangement 35 of the appearance order of map φ [i] t , while the problem can be beaten, e.g., by the mollifying force technique.…”

Section: Distributions Of Variablesmentioning

confidence: 99%

Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations

2008

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This article illustrates practical applications to molecular dynamics simulations of the recently developed numerical integrators [Phys Rev E 2006, 73, 026703] for ordinary differential equations. This method consists of extending any set of ordinary differential equations in order to define a time invariant function, and then use the techniques of divergence-free solvable decomposition and symmetric composition to obtain volume-preserving integrators in the extended phase space. Here, we have developed the technique by constructing multiple extended-variable formalism in order to enhance the handling in actual simulation, and by constituting higher order integrators to obtain further accuracies. Using these integrators, we perform constant temperature molecular dynamics simulations of liquid water, liquid argon and peptide in liquid water droplet. The temperature control is obtained through an extended version of the Nosé-Hoover equations. Analyzing the effects of the simulation conditions including time step length, initial values, boundary conditions, and equation parameters, we investigate local accuracy, global accuracy, computational cost, and sensitivity along with the sampling validity. According to the results of these simulations, we show that the volume-preserving integrators developed by the current method are more effective than traditional integrators that lack the volume-preserving property.

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“…4 Subsequent developments have also cured resonance problems associated with the original method. [5][6][7][8][9] Multiple time stepping does not have the well-known drawback of constraints that averages in the constrained system differ from those of the unconstrained system. 10 However, for complex molecules this is a small effect and constraints might be the preferred option.…”

Section: Introductionmentioning

confidence: 99%

MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes

Bailey

Lowe

2009

J Comput Chem

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We describe a method to impose constraints in a molecular dynamics simulation. A technique developed to solve the special case of a linear topology (MILC SHAKE) is hybridized with the SHAKE algorithm. The methodology, which we term MILC-hybridized SHAKE (or MILCH SHAKE), applies to more complex topologies. Here we consider the important case of all atom models of alkanes. Exploiting the mass difference between carbon and hydrogen we show that for higher alkanes MILCH SHAKE can be an order of magnitude faster than SHAKE.

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Nonlinear Resonance Artifacts in Molecular Dynamics Simulations

Cited by 87 publications

References 28 publications

Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics

Masking Resonance Artifacts in Force-Splitting Methods for Biomolecular Simulations by Extrapolative Langevin Dynamics

Numerical examination of the extended phase‐space volume‐preserving integrator by the Nosé‐Hoover molecular dynamics equations

MILCH SHAKE: An efficient method for constraint dynamics applied to alkanes

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