scholarly journals Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

2009 ◽  
pp. NA-NA ◽  
Author(s):  
Peter Eastman ◽  
Vijay S. Pande
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Nonbonded Interactions ◽  
Graphics Processing

Graphics Processing Unit-Accelerated Semiempirical Born Oppenheimer Molecular Dynamics Using PyTorch

2020 ◽  
Vol 16 (8) ◽  
pp. 4951-4962 ◽  
Author(s):  
Guoqing Zhou ◽  
Ben Nebgen ◽  
Nicholas Lubbers ◽  
Walter Malone ◽  
Anders M. N. Niklasson ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Graphics Processing

scholarly journals Accelerating Molecular Dynamics Simulation Using Graphics Processing Unit

2010 ◽  
Vol 31 (12) ◽  
pp. 3639-3643 ◽  
Author(s):  
Hun-Joo Myung ◽  
Ryuji Sakamaki ◽  
Kwang-Jin Oh ◽  
Tetsu Narumi ◽  
Kenji Yasuoka ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Graphics Processing Unit ◽  
Dynamics Simulation ◽  
Processing Unit ◽  
Graphics Processing

scholarly journals Molecular dynamics simulation of macromolecules using graphics processing unit

2010 ◽  
Vol 36 (14) ◽  
pp. 1131-1140 ◽  
Author(s):  
Ji Xu ◽  
Ying Ren ◽  
Wei Ge ◽  
Xiang Yu ◽  
Xiaozhen Yang ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Graphics Processing Unit ◽  
Dynamics Simulation ◽  
Processing Unit ◽  
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.

A Graphics Processing Unit Implementation of Coulomb Interaction in Molecular Dynamics

2010 ◽  
Vol 6 (10) ◽  
pp. 3058-3065 ◽  
Author(s):  
Prateek K. Jha ◽  
Rastko Sknepnek ◽  
Guillermo Iván Guerrero-García ◽  
Monica Olvera de la Cruz
Keyword(s):  
Molecular Dynamics ◽  
Coulomb Interaction ◽  
Graphics Processing Unit ◽  
Processing Unit ◽  
Graphics Processing
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