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WIREs Comput Mol Sci
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Classical molecular dynamics on graphics processing unit architectures

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Abstract Molecular dynamics (MD) has experienced a significant growth in the recent decades. Simulating systems consisting of hundreds of thousands of atoms is a routine task of computational chemistry researchers nowadays. Thanks to the straightforwardly parallelizable structure of the algorithms, the most promising method to speed‐up MD calculations is exploiting the large‐scale processing power offered by the parallel hardware architecture of graphics processing units or GPUs. Programming GPUs is becoming easier with general‐purpose GPU computing frameworks and higher levels of abstraction. In the recent years, implementing MD simulations on graphics processors has gained a large interest, with multiple popular software packages including some form of GPU‐acceleration support. Different approaches have been developed regarding various aspects of the algorithms, with important differences in the specific solutions. Focusing on published works in the field of classical MD, we describe the chosen implementation methods and algorithmic techniques used for porting to GPU, as well as how recent advances of GPU architectures will provide even more optimization possibilities in the future. This article is characterized under: Software > Simulation Methods Computer and Information Science > Computer Algorithms and Programming Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo Methods
Performance trend for CUDA‐supported NVIDIA GeForce desktop GPUs with regards to single‐precision theoretical peak GFLOPS across different models. The photo in the upper left corner depicts the GeForce GTX 970 GPU by NVIDIA, featuring about 3500 GFLOPS single‐precision processing power and 4 GB memory. GPU, graphics processing unit
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OpenCL architecture. GPU, graphics processing unit
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NVIDIA memory hierarchy
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NVIDIA hardware model. GPU, graphics processing unit
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Software > Simulation Methods
Molecular and Statistical Mechanics > Molecular Dynamics and Monte-Carlo Methods
Computer and Information Science > Computer Algorithms and Programming

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