Parallel implementation of molecular dynamics simulation for short-ranged interaction

Wu, Jong-Shinn; Hsu, Yeh‐Liang; Lee, Yun Min

doi:10.1016/j.cpc.2005.03.110

Cited by 3 publications

(2 citation statements)

References 16 publications

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“…This is similar to domain decomposition, where the particles in the cells at the boundary of a domain are "exported", i.e. copied, to the neighbour domains for the calculation of the forces [19,20,21,22,23,24]. Only interactions with the positive half shell of surrounding cells are computed, so Newton's third law is exploited to avoid the calculation of an interaction twice.…”

Section: Minimum Image Conventionmentioning

confidence: 99%

Efficiency of linked cell algorithms

Welling

Germano

2011

Computer Physics Communications

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The linked cell list algorithm is an essential part of molecular simulation software, both molecular dynamics and Monte Carlo. Though it scales linearly with the number of particles, there has been a constant interest in increasing its efficiency, because a large part of CPU time is spent to identify the interacting particles. Several recent publications proposed improvements to the algorithm and investigated their efficiency by applying them to particular setups. In this publication we develop a general method to evaluate the efficiency of these algorithms, which is mostly independent of the parameters of the simulation, and test it for a number of linked cell list algorithms. We also propose a combination of linked cell reordering and interaction sorting that shows a good efficiency for a broad range of simulation setups.Comment: Submitted to Computer Physics Communications on 22 December 2009, still awaiting a referee repor

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Section: Minimum Image Conventionmentioning

confidence: 99%

Efficiency of linked cell algorithms

Welling

Germano

2011

Computer Physics Communications

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“…El diseño de drogas es comúnmente usado en la industria farmacéutica para probar las propiedades de una molécula en el computador sin necesidad de sintetizarla (lo cual es mucho más costoso) [57]. Ha sido ampliamente usada para simular propiedades de los líquidos, sólidos, y moléculas en investigaciones de diversas disciplinas, incluyendo las ciencias de los materiales, tecnología biológica, transferencia de calor y masa, entre otras [61].…”

Section: Dinámica Molecular Computacionalunclassified

Computación de alto desempeño aplicada en técnicas de simulación de proteínas

Pachón¹

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Se busca estudiar alternativas de computación de alto desempeño (HPC) viables en la PUJ para generar opciones que permitan potenciar la e-Science y el trabajo interdisciplinario. Para ello se revisó el estado del arte y la necesidad de HPC, observando posibles problemas que demuestren las ventajas de tener un sistema con estas características, se diseñó un experimento de simulación utilizando clusters computacionales diferenciados según capacidad y cantidad de procesadores| se seleccionaron las moléculas según resultados experimentales, se seleccionaron variables independientes, dependientes e intervinientes para preparar y configurar las simulaciones. Se desarrollaron scripts y programas para replicar configuraciones en las máquinas.

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Parallel node placement method by bubble simulation

Nie

Zhang

et al. 2014

Computer Physics Communications

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Parallel implementation of molecular dynamics simulation for short-ranged interaction

Cited by 3 publications

References 16 publications

Efficiency of linked cell algorithms

Efficiency of linked cell algorithms

Computación de alto desempeño aplicada en técnicas de simulación de proteínas

Parallel node placement method by bubble simulation

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