Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within the<i>e</i>Minerals escience project

Dove, Martin T.; Sullivan, L. A.; Walker, Andrew; Bruin, R. P.; White, T. O. H.; Trachenko, Kostya; Murray‐Rust, Peter; Todorov, Ilian T.; Tyer, R. P.; Couch, Philip; Dam, Kerstin Kleese van; Smith, William R.

doi:10.1080/08927020600883293

Cited by 9 publications

(5 citation statements)

References 22 publications

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“…This approach minimizes the effects of statistical errors on the individual points, but requires the large number of points shown in the graph. The analysis of the configurations showed clearly that the enhanced compressibility arises from the flexibility of the silica network that is lost under extreme compression or expansion, in line with the original hypothesis (Dove et al 2006;Walker et al 2007).…”

Section: (B ) Simulation Studies Of Radiation Damage and Nuclear Waste Encapsulationsupporting

confidence: 76%

eScience for molecular-scale simulations and the e Minerals project

Salje

Artacho

Austen

et al. 2008

Phil. Trans. R. Soc. A.

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We review the work carried out within the eMinerals project to develop eScience solutions that facilitate a new generation of molecular-scale simulation work. Technological developments include integration of compute and data systems, developing of collaborative frameworks and new researcher-friendly tools for grid job submission, XML data representation, information delivery, metadata harvesting and metadata management. A number of diverse science applications will illustrate how these tools are being used for large parameter-sweep studies, an emerging type of study for which the integration of computing, data and collaboration is essential.

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Section: (B ) Simulation Studies Of Radiation Damage and Nuclear Waste Encapsulationsupporting

confidence: 76%

eScience for molecular-scale simulations and the e Minerals project

Salje

Artacho

Austen

et al. 2008

Phil. Trans. R. Soc. A.

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“…This was performed using the microcanonical (NVE) ensemble, and used for analysis of the dynamics of the glass model. By using grid computing [19][20][21][22] and data management methods [21][22][23] we were able to run many more simulations than would be normal for this type of study. Pressures were varied between −5 and +5 GPa.…”

Section: Methodsmentioning

confidence: 99%

The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study

Walker¹,

Sullivan²,

Trachenko³

et al. 2007

J. Phys.: Condens. Matter

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We propose an explanation for the anomalous compressibility maximum in amorphous silica based on rigidity arguments. The model considers the fact that a network structure will be rigidly compressed in the high-pressure limit, and rigidly taut in the negative pressure limit, but flexible and hence softer at intermediate pressures. We validate the plausibility of this explanation by the analysis of molecular dynamics simulations. In fact this model is quite general, and will apply to any network solid, crystalline or amorphous; there are experimental indications that support this prediction. In contrast to other ideas concerning the compressibility maximum in amorphous silica, the model presented here does not invoke the existence of polyamorphic phase transitions in the glass phase.

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“…To monitor the time evolution of the MD simulation and to compute averages we used our dlparse program to general an XML file for each run based on the Chemical Markup Language, 38,39 which was transformed to an XHTML file easy viewing using our ccViz program. 40 To extract and collate averages from the many files generated in a suite of simulations across many temperatures, such as average lattice parameters at each temperature, we created a Fortran program using the FoX XML libraries.…”

Section: Molecular Dynamics Simulationsmentioning

confidence: 99%

Molecular dynamics simulation study of various zeolitic imidazolate framework structures

et al. 2016

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We report the results of a series of molecular dynamics simulations on a number of zinc zeolitic imidazolate framework (ZIF) structures together with some lattice dynamics calculations on ZIF-4, providing information about the flexibilities of these structures. The simulations have used a force field we developed based on ab initio calculations of clusters of ligands and metal cations. We have shown that there are instabilities of the structures of some ZIF structures at low temperatures and high pressures. A rigidity analysis based on the Rigid Unit Mode model shows considerable degree of network flexibility, including a significant elastic flexibility.

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Molecular dynamics in a grid computing environment: experiences using DL_POLY_3 within theeMinerals escience project

Cited by 9 publications

References 22 publications

eScience for molecular-scale simulations and the e Minerals project

eScience for molecular-scale simulations and the e Minerals project

The origin of the compressibility anomaly in amorphous silica: a molecular dynamics study

Molecular dynamics simulation study of various zeolitic imidazolate framework structures

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