A flexible algorithm for calculating pair interactions on SIMD architectures
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TLDR
This work presents an algorithm for SIMD parallelization based on grouping a fixed number of particles, e.g. 2, 4, or 8, into spatial clusters, which improves data reuse compared to the traditional scheme and results in a more efficient SIMD Parallelization.About:
This article is published in Computer Physics Communications.The article was published on 2013-12-01 and is currently open access. It has received 524 citations till now. The article focuses on the topics: SIMD & Xeon Phi.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
GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers
Mark Abraham,Teemu Murtola,Roland Schulz,Roland Schulz,Szilárd Páll,Jeremy C. Smith,Jeremy C. Smith,Berk Hess,Erik Lindahl,Erik Lindahl +9 more
TL;DR: GROMACS is one of the most widely used open-source and free software codes in chemistry, used primarily for dynamical simulations of biomolecules, and provides a rich set of calculation types.
Book ChapterDOI
Tackling Exascale Software Challenges in Molecular Dynamics Simulations with GROMACS
TL;DR: GROMACS as mentioned in this paper is a widely used package for biomolecular simulation, and over the last two decades it has evolved from small-scale efficiency to advanced heterogeneous acceleration and multi-level parallelism targeting some of the largest supercomputers in the world.
Journal ArticleDOI
Strong scaling of general-purpose molecular dynamics simulations on GPUs
Jens Glaser,Trung Dac Nguyen,Joshua A. Anderson,Pak Lui,Filippo Spiga,Jaime A. Millan,David C. Morse,Sharon C. Glotzer +7 more
TL;DR: A highly optimized implementation of MPI domain decomposition in a GPU-enabled, general-purpose molecular dynamics code, HOOMD-blue, which achieves optimal GPU performance using an autotuning algorithm.
Book ChapterDOI
Molecular Dynamics Simulation
TL;DR: This section provides a compact description of the basics of MD simulation, and focuses on single- and multi-center interactions based on the Lennard-Jones potential for short-range interactions.
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
Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
TL;DR: In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.
Journal ArticleDOI
A smooth particle mesh Ewald method
TL;DR: It is demonstrated that arbitrary accuracy can be achieved, independent of system size N, at a cost that scales as N log(N), which is comparable to that of a simple truncation method of 10 A or less.
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.