General purpose molecular dynamics simulations fully implemented on graphics processing units

Anderson, Jon; Lorenz, Christian D.; Travesset, Alex

doi:10.1016/j.jcp.2008.01.047

Cited by 1,410 publications

(1,171 citation statements)

References 17 publications

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“…Two related continuum models were also simulated using molecular dynamics (MD) simulations for comparison with the lattice model. We used the HOOMD (Highly Optimized Object-oriented Many-particle Dynamics) package [31,32] which takes advantage of graphics processing units (GPUs) to accelerate the simulation of large systems [33]. All athermal interactions were approximated through the use of a LennardJones potential cut off at the minimum,…”

Section: Methodsmentioning

confidence: 99%

Structure of phase-separated athermal colloid-polymer systems in the protein limit

2013

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Structural features of phase separated athermal colloid-polymer mixtures in the so-called "protein limit," where polymer chain dimensions exceed those of the colloid, are investigated using grand canonical Monte Carlo simulations on a fine lattice. Previous work [N. A. Mahynski, et al. Phys. Rev. E 85, 051402 (2012)] has shown that this model accurately captures the phase behavior of experimental systems, and that colloids with sufficiently small diameters, σc, relative to that of the monomeric segments, σs, phase separate more readily than their large-diameter counterparts. In the present study, we directly connect colloid and polymer structure with their phase behavior by investigating these solutions along their binodal curves; we also explore the role of colloid surface curvature in destabilizing such solutions. Our findings suggest that simple consideration of an additional depletion radius, on the order of the σs, leads to a quantitatively accurate prediction of the division between stable and unstable ranges of d = σs/σc. We compare these results to continuum models with different bonding potentials between monomer segments in order to elucidate the significance of the lattice model's bond fluctuations and inherently coarse colloid surface. In a number of cases, the continuum models deviate both qualitatively and quantitatively from the lattice results, but the binodals of the continuum models are presently not known, making a strong conclusion about these differences impossible.

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Section: Methodsmentioning

confidence: 99%

Structure of phase-separated athermal colloid-polymer systems in the protein limit

2013

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“…55,56 This model is studied by standard MD methods, 58,59 using graphics processing units (GPUs) employing the HOOMDblue software package. 60,61 The standard velocity Verlet algorithm 58,59 is used to integrate Newton's equations of motion, employing a time step ∆t = 10 −2 τ MD with an intrinsic MD time unit of τ MD = (mσ 2 / ) 1/2 . To maintain constant temperature (and hence realize the NVT ensemble with a volume V = 4πR 3 /3), we employ a Langevin thermostat 40,41 with a friction coefficient γ = 0.25.…”

Section: A Molecular Dynamicsmentioning

confidence: 99%

Conformations and orientational ordering of semiflexible polymers in spherical confinement

Milchev

Егоров

Nikoubashman

et al. 2017

The Journal of Chemical Physics

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Semiflexible polymers in lyotropic solution confined inside spherical nanoscopic "containers" with repulsive walls are studied by molecular dynamics simulations and density functional theory, as a first step to model confinement effects on stiff polymers inside of miniemulsions, vesicles, and cells. It is shown that the depletion effects caused by the monomer-wall repulsion depend distinctly on the radius R of the sphere. Further, nontrivial orientational effects occur when R, the persistence length p , and the contour length L of the polymers are of similar magnitude. At intermediate densities, a "shell" of wallattached chains is forming, such that the monomers belonging to those chains are in a layer at about the distance of one monomer from the container wall. At the same time, the density of the centers of mass of these chains is peaked somewhat further inside, but still near the wall. However, the arrangement of chains is such that the total monomer density is almost uniform in the sphere, apart from a small layering peak at the wall. It is shown that excluded volume effects among the monomers are crucial to account for this behavior, although they are negligible for comparable isolated single semiflexible chains of the same length. Published by AIP Publishing. [http://dx

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“…The equilibrium equations applied to control points of the whole domain are expressed as K u=f (12) In order to formulate the total stiffness matrix, the stiffness matrix of every patch i=1, … , N p has to be calculated:…”

Section: Stiffness Matrix Formulationmentioning

confidence: 99%

Computation of the Isogeometric Analysis Stiffness Matrix on Gpu

Karatarakis¹,

Karakitsios²,

Papadrakakis³

2013

Proceedings of the 3rd South-East European Conference on Computational Mechanics – SEECCM III

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General purpose molecular dynamics simulations fully implemented on graphics processing units

Cited by 1,410 publications

References 17 publications

Structure of phase-separated athermal colloid-polymer systems in the protein limit

Structure of phase-separated athermal colloid-polymer systems in the protein limit

Conformations and orientational ordering of semiflexible polymers in spherical confinement

Computation of the Isogeometric Analysis Stiffness Matrix on Gpu

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