LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Thompson, Aidan P.; Aktulga, Hasan Metin; Berger, Richard A.; Bolintineanu, Dan; Brown, William M.; Crozier, Paul; Veld, Pieter J. in ’t; Kohlmeyer, Axel; Moore, Stan Gerald; Nguyen, Trung Dac; Shan, Ray; Stevens, Mark J.; Tranchida, Julien; Trott, Christian Robert; Plimpton, Steven J.

doi:10.1016/j.cpc.2021.108171

Cited by 3,455 publications

(1,600 citation statements)

References 240 publications

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“…We simulate the system with LAMMPS, adopting the Nose–Hoover thermostat and barostat, 123 with relaxation time 10 2 and 10 3 MD steps, respectively, and with 10 5 MD steps of relaxation, enough to reach equilibrium in the bulk and within the confined subregion. Next we compute the observables for 10 5 more MD steps, recording each quantity every 10 3 MD steps.…”

Section: Methodsmentioning

confidence: 99%

“…We adopt the same slit-pore as for the LJ fluid with the weak fluid-wall interaction, ϵ w 1 = 0.1 kcal/mol, simulating the system with LAMMPS and Nose–Hoover thermostat, 123 with the same equilibration and production statistics as for the LJ. We perform the simulations at constant number N tot = 25000 of CSW particles, constant temperature T , and constant box volume V , leaving the bulk pressure P bulk free to change (simulations at constant P bulk for the CSW fluid at the same T , same P bulk , and same N tot as for the LJ fluid would require a much larger box for the CSW than the LJ in order to get a comparable number of particles inside the subvolume V s ).…”

Section: Methodsmentioning

confidence: 99%

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Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

2021

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Nanoconfinement can drastically change the behavior of liquids, puzzling us with counterintuitive properties. It is relevant in applications, including decontamination and crystallization control. However, it still lacks a systematic analysis for fluids with different bulk properties. Here we address this gap. We compare, by molecular dynamics simulations, three different liquids in a graphene slit pore: (1) A simple fluid, such as argon, described by a Lennard-Jones potential; (2) an anomalous fluid, such as a liquid metal, modeled with an isotropic core-softened potential; and (3) water, the prototypical anomalous liquid, with directional HBs. We study how the slit-pore width affects the structure, thermodynamics, and dynamics of the fluids. All the fluids show similar oscillating properties by changing the pore size. However, their free-energy minima are quite different in nature: (i) are energy-driven for the simple liquid; (ii) are entropy-driven for the isotropic core-softened potential; and (iii) have a changing nature for water. Indeed, for water, the monolayer minimum is entropy driven, at variance with the simple liquid, while the bilayer minimum is energy driven, at variance with the other anomalous liquid. Also, water has a large increase in diffusion for subnm slit pores, becoming faster than bulk. Instead, the other two fluids have diffusion oscillations much smaller than water, slowing down for decreasing slit-pore width. Our results, clarifying that water confined at the subnm scale behaves differently from other (simple or anomalous) fluids under similar confinement, are possibly relevant in nanopores applications, for example, in water purification from contaminants.

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Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

2021

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“…These structures are solvated in SPC/E water [52] with the aid of the software PACKMOL [53,54]. All files are transferred to the open-source simulation package LAMMPS, in which the equilibration and production runs are performed [55,56].…”

Section: Simulation Modelmentioning

confidence: 99%

Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

2021

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We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

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“…To study the system, fully atomistic MD simulations are employed. All simulation runs are carried out in the open-source simulation software LAMMPS [52,53]. The TrisAzo molecules are parameterized in the DREIDING force field [54].…”

Section: Basic Simulation Modelmentioning

confidence: 99%

“…Coulomb interactions are evaluated via the PPPM algorithm with an accuracy of 10 −4 [63,64]. Ther-mostatting, barostatting, and time-integration are carried out via a Nosé-Hoover-style algorithm as implemented in LAMMPS [52,53]. Temperature and pressure are kept at constant average values of T = 300 K and P = 1 atm (NPT ensemble), respectively, to match the experimental conditions of Ref.…”

Section: Basic Simulation Modelmentioning

confidence: 99%

Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

2021

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This computational study investigates the influence of light on supramolecular aggregates of three-arm azobenzene stars. Every star contains three azobenzene (azo) moieties, each able to undergo reversible photoisomerization. In solution, the azo stars build column-shaped supramolecular aggregates. Previous experimental works report severe morphological changes of these aggregates under UV–Vis light. However, the underlying molecular mechanisms are still debated. Here we aim to elucidate how light affects the structure and stability of the columnar stacks on the molecular scale. The system is investigated using fully atomistic molecular dynamics (MD) simulations. To implement the effects of light, we first developed a stochastic model of the cyclic photoisomerization of azobenzene. This model reproduces the collective photoisomerization kinetics of the azo stars in good agreement with theory and previous experiments. We then apply light of various intensities and wavelengths on an equilibrated columnar stack of azo stars in water. The simulations indicate that the aggregate does not break into separate fragments upon light irradiation. Instead, the stack develops defects in the form of molecular shifts and reorientations and, as a result, it eventually loses its columnar shape. The mechanism and driving forces behind this order–disorder structural transition are clarified based on the simulations. In the end, we provide a new interpretation of the experimentally observed morphological changes.

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LAMMPS - a flexible simulation tool for particle-based materials modeling at the atomic, meso, and continuum scales

Cited by 3,455 publications

References 240 publications

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

Nanoconfined Fluids: Uniqueness of Water Compared to Other Liquids

Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

Cyclic Photoisomerization of Azobenzene in Atomistic Simulations: Modeling the Effect of Light on Columnar Aggregates of Azo Stars

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