Molecular dynamics is a widely used simulation method, which, together with electronic structure methods, quantum dynamics, and Brownian dynamics, plays an important role in modeling processes at the atomic level. Molecular dynamics is also a widely studied method. To model systems more accurately and for longer time scales with improved turn--around time, scientists continually seek efficient algorithms to utilize fully modern computing resources. Because it is a computationally challenging application of importance, molecular dynamics is often used to evaluate computing systems, placing it in benchmark suites such as SPEC (System Performance and Evaluation Cooperative) and SPLASH [28]. As a benchmark, MD is often used alongside other applications to evaluate computer
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705
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SPLASH: Stanford Parallel Applications for Shared Memory
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333
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Limits of Instruction-Level Parallelism
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90
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86
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84
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Fast parallel algorithms for short-range molecular dynamics
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78
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Jade: A high-level, machine-independent language for parallel programming
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70
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Working sets, cache sizes, and node granularity issues for large-scale multiprocessors
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68
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58
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GROMOS: GROningen MOlecular Simulation software
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30
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Parallelizing molecular dynamics using spatial decomposition
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30
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Generalized Verlet algorithm for efficient molecular dynamics simulations with long-range interactions
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23
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Parallelization of charmm for mimd machines
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21
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15
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Evaluating parallel languages for molecular dynamics computations
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14
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13
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Parallelization of a molecular dynamics non-bonded force algorithm for MIMD architectures
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12
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Large scale molecular dynamics on parallel computers using the link-cell algorithm
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11
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Compiler Support for Machine-Independent Parallelization of Irregular Problems
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10
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Efficient Parallel Implementation of Molecular Dynamics on a Toroidal Network: I. Parallelizing strategy
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9
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AMBERCUBE MD, parallelization of AMBER's molecular dynamics module for distributed--memory hypercube computers
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8
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7
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7
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5
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Multi-colour algorithms in molecular simulation: Vectorisation and parallelisation of internal forces and constraints
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5
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ARGOS, a vectorized general molecular dynamics program
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5
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On searching neighbors in computer simulations of macromolecular systems
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3
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A vectorized "near neighbors" algorithm of order n using a monotonic logical grid
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3
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I/O limitations in parallel molecular dynamics
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2
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Experiences in data-parallel programming
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1
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1
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1
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The DASH protoptype: logic overhead and performance
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