Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

Grubmüller, Helmut; Heller, Helmut; Windemuth, Andreas; Schulten, Klaus

doi:10.1080/08927029108022142

Cited by 526 publications

(433 citation statements)

References 8 publications

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“…Short-range real-space interactions were cut off at 11 Å, employing a switching function. A reversible multiple time-step algorithm 57 was employed to integrate the equations of motion with a time step of 2 fs for electrostatic forces, 1 fs for short-range nonbonded forces, and 1 fs for bonded forces. Snapshots were saved at 1 ps intervals for detailed analysis.…”

Section: ■ Introductionmentioning

confidence: 99%

Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films

et al. 2012

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Understanding the interactions of humid air with ionic liquids (ILs) is critical for predicting how their physicochemical properties are affected by water. Using experimental and theoretical techniques, water vapor's interaction with aerosolized nanoparticles and thin films of [C 2 MIM][Cl] and [C 2 MIM][BF 4 ] was studied. Solutions were electrosprayed to produce dry particles. Particles' hygroscopic growth was quantified using tandem nanodifferential mobility analysis as a function of relative humidity (RH). This is the first report of the interaction of water with aerosolized IL nanoparticles. The particles' small size allows true IL−water vapor equilibrium achieved quickly. Growth curves for both ILs show steady water uptake with increasing RH. Water vapor uptake by IL thin films was also examined using ATR-FTIR spectroscopy. . They represent a large class of molecules that have unique and widely tunable physical and chemical properties. 1−3 For example, there is a significant interest in the use of ILs in green chemistry, 2,4,5 due to their negligible vapor pressure at room temperature, 6 and for many other applications including solvents in synthesis and catalysis, 1,6 chemical extraction, 1,2,5 and fuel cells. 7 Physical properties such as conductivity, viscosity, density, and surface tension of ILs are known to depend on the presence of water, both adsorbed and absorbed. 3,8 Water is ubiquitous in the environment, and hygroscopic ILs such as those with imidazolium-based cations can uptake significant amounts of water vapor from ambient air, which alters their physical and chemical properties. 1,3 Thus, quantification of water uptake by hygroscopic ILs and understanding how the presence of water affects the nature of the ion−ion and ion−water interactions are critical for use of ILs in future applications. 8−14 Numerous experimental and theoretical studies have investigated the interaction of imidazolium-based ILs with water. 3,8−35 It is understood that both the cation and the anion have an effect on how ILs interact with water, with the anion having a stronger effect. 3,17,19 Early experimental work by Seddon et al. investigated the miscibility of water with ILs containing 1-nalkyl-3-methylimidazolium ([C n MIM + ], n = number of carbons on the linear alkyl chain) cations and various anions at room temperature. 3 It was determined that, regardless of the alkyl chain length, all halide anions were fully soluble in water and all hexafluorophosphate ([PF 6 − ]) anions were insoluble. 3 However, alkyl chain length did have an effect on water miscibility of [C n MIM + ]-based ILs with tetrafluoroborate ([BF 4 − ]) anions; for chain lengths of n = 2 or 4, the ILs were fully miscible, but for n > 4, the ILs formed biphasic systems. 3 Cammarata et al. performed early attenuated total reflection (ATR) infrared (IR) studies on the molecular states of water

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Section: ■ Introductionmentioning

confidence: 99%

Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films

et al. 2012

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“…In the MTS molecular dynamics simulations, the interatomic forces are split into the fast and slow components corresponding to the short and long range forces, respectively [1][2][3][4]. In the standard MD simulations, the forces must be recomputed at each time step [5].…”

Section: Introductionmentioning

confidence: 99%

“…To simulate deformations under realistic applied loading rate from 10 -6 /s to 10 6 /s with molecular simulation is desired but not yet available, although some techniques, like the Multiple Time-Step (MTS) method [1][2][3][4], have been developed. Therefore, to explore how to split and combine the fast and slow motions, namely the high frequency (thermal) motion with atomic frequency of about 10 13 /s and the low frequency deformation of atomic lattice, is a key to this multiple-time scale problem.…”

Section: Introductionmentioning

confidence: 99%

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

Zheng¹,

Bai²

2010

AIP Conference Proceedings

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Abstract. The atomic motion is coupled by the fast and slow components due to the high frequency vibration of atoms and the low frequency deformation of atomic lattice, respectively. A two-step approximate method was presented to determine the atomic slow motion. The first step is based on the change of the location of the cold potential well bottom and the second step is based on the average of the appropriate slow velocities of the surrounding atoms. The simple tensions of one-dimensional atoms and two-dimensional atoms were performed with the full molecular dynamics simulations. The conjugate gradient method was employed to determine the corresponding location of cold potential well bottom. Results show that our two-step approximate method is appropriate to determine the atomic slow motion under the low strain rate loading. This splitting method may be helpful to develop more efficient molecular modeling methods and simulations pertinent to realistic loading conditions of materials.

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“…A variety of more elaborate multiple-timestep approaches have been proposed including the Verlet-I scheme 111 and the reversible reference system propagation algorithm (r-RESPA) 112 . These methods apply the low-frequency forces as a periodic impulse whenever they are evaluated.…”

Section: Discussionmentioning

confidence: 99%

Improving the accuracy of molecular dynamics simulations: parameterisation of interaction potentials for small molecules

Stroet¹

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The ability to accurately describe molecular systems with classical molecular dynamics (MD) is critically dependent on an understanding of the sources of error in the design, evaluation and analysis of the underlying model. One significant source of error is in the degree to which the equations and parameters used to represent atomic interaction can reproduce the experimental properties relevant to a particular application. While highly optimised and well-validated interaction parameters are available for common biomolecules (amino acids, sugars, lipids etc.), this is not the case for heterogeneous small molecules such as co-factors, substrates and drugs. The enormity of the chemical space covered by small molecules necessitates the development of automated approaches to parameterising and validating interaction parameters. Several tools are available that can be used to generate interaction parameters for small molecules compatible with a particular existing (bio)molecular force field. Despite their popularity, many are poorly validated, while some have been shown to be inappropriate for many applications. In other cases, validation studies have demonstrated reasonable performance, however, they also suggest significant improvements can be made. One such tool is the Automated Topology Builder (ATB, http://atb.uq.edu.au/) which provides interaction parameters for small molecules compatible with the GROMOS biomolecular force field.As part of this work, a fully automated protocol for the calculation of solvation energy by thermodynamic integration has been developed and applied to the large-scale validation of the ATB against experimental solvation data in water and hexane. It is shown that the largest errors are due to the Lennard-Jones parameters used for functional groups not present in common biomolecules. Other sources of error included the atomic charges assigned by the ATB for the united atom carbons and incompatibilities between GROMOS Lennard-Jones parameters and the ATB charge model. Significant sources of error were also identified in the evaluation of MD models, both for the calculation of solvation energy as well as for MD simulations of lipid membranes. In particular, the use of multiple-time-step algorithms as a time-saving technique. For the calculation of solvation energy by TI, the twin-range cutoff scheme-commonly used in simulations with the GROMOS force field-was found to introduce a systematic error of about 1 kJ/mol. While for lipid systems, various III changes made to the integration algorithm of the GROMACS simulation code were found to significantly alter the properties of lipid membranes when simulated with identical force fields.Finally, a method for parameterising transferrable interaction potentials with respect to a wide range of target properties is presented. The method is based on an analysis of surfaces corresponding to the difference between calculated and target data as a function of alternative combinations of parameters.The consideration of surfaces in parameter space...

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Generalized Verlet Algorithm for Efficient Molecular Dynamics Simulations with Long-range Interactions

Cited by 526 publications

References 8 publications

Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films

Interaction of Water Vapor with the Surfaces of Imidazolium-Based Ionic Liquid Nanoparticles and Thin Films

Splitting the Fast and Slow Motions in Molecular Dynamics Simulations Based on the Change of Cold Potential Well Bottom

Improving the accuracy of molecular dynamics simulations: parameterisation of interaction potentials for small molecules

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