Journal ArticleDOI
GPU implementations of some many-body potentials for molecular dynamics simulations
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TLDR
It is shown that Tersoff potential can be computed faster using atomic operations rather than using longer kernel code, and better performance can be gained for embedded-atom potential without atomic operations.About:
This article is published in Advances in Engineering Software.The article was published on 2017-09-01. It has received 9 citations till now.read more
Citations
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Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Journal ArticleDOI
Design, Parameterization, and Implementation of Atomic Force Fields for Adsorption in Nanoporous Materials
TL;DR: In this article, a review of the development, parameterization, and implementation of force fields for metal-organic frameworks (MOFs) and zeolites can be found, along with an overview of recent developments in force field design and implementation.
Journal ArticleDOI
50 million atoms scale molecular dynamics modelling on a single consumer graphics card
TL;DR: A dynamic cell-list method for realizing large scale molecular dynamics simulations with more than 50 million atoms on a single consumer graphics card by introducing an efficient two-step atom location scheme and a dynamic memory allocation scheme such that only those cells containing atoms consume device memory.
Journal ArticleDOI
Classical molecular dynamics on graphics processing unit architectures
TL;DR: Focusing on published works in the field of classical MD, the chosen implementation methods and algorithmic techniques used for porting to GPU are described, as well as how recent advances of GPU architectures will provide even more optimization possibilities in the future.
Book ChapterDOI
GPU-Accelerated Molecular Dynamics: Energy Consumption and Performance
Vyacheslav S. Vecher,Vyacheslav S. Vecher,Vsevolod Nikolskii,Vsevolod Nikolskii,Vladimir V. Stegailov +4 more
TL;DR: This paper discusses the energy and power efficiency of two modern hybrid minicomputers Jetson TK1 and TX1, using the Empirical Roofline Tool to obtain peak performance data and the molecular dynamics package LAMMPS as an example of a real-world benchmark.
References
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Journal ArticleDOI
Fast parallel algorithms for short-range molecular dynamics
TL;DR: In this article, three parallel algorithms for classical molecular dynamics are presented, which can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
Journal ArticleDOI
Matplotlib: A 2D Graphics Environment
TL;DR: Matplotlib is a 2D graphics package used for Python for application development, interactive scripting, and publication-quality image generation across user interfaces and operating systems.
Book
Computer Simulation of Liquids
Michael P. Allen,D. J. Tildesley +1 more
TL;DR: In this paper, the gear predictor -corrector is used to calculate forces and torques in a non-equilibrium molecular dynamics simulation using Monte Carlo methods. But it is not suitable for the gear prediction problem.
Journal ArticleDOI
Scalable molecular dynamics with NAMD
James C. Phillips,Rosemary Braun,Wei Wang,James C. Gumbart,Emad Tajkhorshid,Elizabeth Villa,Christophe Chipot,Robert D. Skeel,Laxmikant V. Kale,Klaus Schulten +9 more
TL;DR: NAMD as discussed by the authors is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems that scales to hundreds of processors on high-end parallel platforms, as well as tens of processors in low-cost commodity clusters, and also runs on individual desktop and laptop computers.