Graphics Processing Unit Acceleration and Parallelization of GENESIS for Large-Scale Molecular Dynamics Simulations

2016 ◽  
Vol 12 (10) ◽  
pp. 4947-4958 ◽  
Author(s):  
Jaewoon Jung ◽  
Akira Naurse ◽  
Chigusa Kobayashi ◽  
Yuji Sugita
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Dynamics Simulations ◽  
Graphics Processing

scholarly journals High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers

2020 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Andrea Browning ◽  
Alexander Goldberg ◽  
Mathew D. Halls ◽  
Jacob L. Gavartin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Specific Volume ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Molecular Systems ◽  
Branched Polyethylene ◽  
Wide Range ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Graphics Processing

Recent advances in graphics-processing-unit (GPU) hardware and improved efficiencies of atomistic simulation programs allow the screening of a large number of polymers to predict properties that require running and analyzing long Molecular Dynamics (MD) trajectories of large molecular systems. This paper outlines an efficient MD cooling simulation workflow based on GPU MD simulation and the refined Optimized Potentials for Liquids Simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (T<sub>g</sub>) of 315 polymers for which experimental values were reported by Bicerano.<sup>1</sup> We observed good agreement of predicted T<sub>g</sub> values with experimental observation across a wide range of polymers, which confirms the clear utility of the described workflow. During the stepwise cooling simulation for the calculation of T<sub>g</sub>, a subset of polymers clearly showed an ordered structure developing as the temperature decreased. Such polymers have a point of discontinuity on the specific volume vs. temperature plot, which we associated with the melting temperature (T<sub>m</sub>). We demonstrate the distinction between crystallized and amorphous polymers by examining polyethylene. Linear polyethylene shows a discontinuity in the specific volume vs. temperature plot, but we do not observe the discontinuity for branched polyethylene simulations.

scholarly journals High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers

2020 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Andrea Browning ◽  
Alexander Goldberg ◽  
Mathew D. Halls ◽  
Jacob L. Gavartin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Specific Volume ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Molecular Systems ◽  
Branched Polyethylene ◽  
Wide Range ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Graphics Processing

Recent advances in graphics-processing-unit (GPU) hardware and improved efficiencies of atomistic simulation programs allow the screening of a large number of polymers to predict properties that require running and analyzing long Molecular Dynamics (MD) trajectories of large molecular systems. This paper outlines an efficient MD cooling simulation workflow based on GPU MD simulation and the refined Optimized Potentials for Liquids Simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (T<sub>g</sub>) of 315 polymers for which experimental values were reported by Bicerano.<sup>1</sup> We observed good agreement of predicted T<sub>g</sub> values with experimental observation across a wide range of polymers, which confirms the clear utility of the described workflow. During the stepwise cooling simulation for the calculation of T<sub>g</sub>, a subset of polymers clearly showed an ordered structure developing as the temperature decreased. Such polymers have a point of discontinuity on the specific volume vs. temperature plot, which we associated with the melting temperature (T<sub>m</sub>). We demonstrate the distinction between crystallized and amorphous polymers by examining polyethylene. Linear polyethylene shows a discontinuity in the specific volume vs. temperature plot, but we do not observe the discontinuity for branched polyethylene simulations.

High-Throughput Molecular Dynamics Simulations and Validation of Thermophysical Properties of Polymers

2020 ◽  
Author(s):  
Mohammad Atif Faiz Afzal ◽  
Andrea Browning ◽  
Alexander Goldberg ◽  
Mathew D. Halls ◽  
Jacob L. Gavartin ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Specific Volume ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Molecular Systems ◽  
Branched Polyethylene ◽  
Wide Range ◽  
Experimental Values ◽  
Dynamics Simulations ◽  
Graphics Processing

Recent advances in graphics-processing-unit (GPU) hardware and improved efficiencies of atomistic simulation programs allow the screening of a large number of polymers to predict properties that require running and analyzing long Molecular Dynamics (MD) trajectories of large molecular systems. This paper outlines an efficient MD cooling simulation workflow based on GPU MD simulation and the refined Optimized Potentials for Liquids Simulation (OPLS) OPLS3e force field to calculate glass transition temperatures (T<sub>g</sub>) of 315 polymers for which experimental values were reported by Bicerano.<sup>1</sup> We observed good agreement of predicted T<sub>g</sub> values with experimental observation across a wide range of polymers, which confirms the clear utility of the described workflow. During the stepwise cooling simulation for the calculation of T<sub>g</sub>, a subset of polymers clearly showed an ordered structure developing as the temperature decreased. Such polymers have a point of discontinuity on the specific volume vs. temperature plot, which we associated with the melting temperature (T<sub>m</sub>). We demonstrate the distinction between crystallized and amorphous polymers by examining polyethylene. Linear polyethylene shows a discontinuity in the specific volume vs. temperature plot, but we do not observe the discontinuity for branched polyethylene simulations.

scholarly journals Large-scale molecular dynamics simulations of TiN/TiN(001) epitaxial film growth

2016 ◽  
Vol 34 (4) ◽  
pp. 041509 ◽  
Author(s):  
Daniel Edström ◽  
Davide G. Sangiovanni ◽  
Lars Hultman ◽  
Ivan Petrov ◽  
J. E. Greene ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Epitaxial Film ◽  
Film Growth ◽  
Dynamics Simulations ◽  
Epitaxial Film Growth

scholarly journals A lightweight approach to performance portability with targetDP

2016 ◽  
Vol 32 (2) ◽  
pp. 288-301
Author(s):  
Alan Gray ◽  
Kevin Stratford
Keyword(s):  
Particle Physics ◽  
Message Passing ◽  
Graphics Processing Units ◽  
High Performance ◽  
Large Scale ◽  
Message Passing Interface ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Performance Portability ◽  
Graphics Processing

Leading high performance computing systems achieve their status through use of highly parallel devices such as NVIDIA graphics processing units or Intel Xeon Phi many-core CPUs. The concept of performance portability across such architectures, as well as traditional CPUs, is vital for the application programmer. In this paper we describe targetDP, a lightweight abstraction layer which allows grid-based applications to target data parallel hardware in a platform agnostic manner. We demonstrate the effectiveness of our pragmatic approach by presenting performance results for a complex fluid application (with which the model was co-designed), plus separate lattice quantum chromodynamics particle physics code. For each application, a single source code base is seen to achieve portable performance, as assessed within the context of the Roofline model. TargetDP can be combined with Message Passing Interface (MPI) to allow use on systems containing multiple nodes: we demonstrate this through provision of scaling results on traditional and graphics processing unit-accelerated large scale supercomputers.

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