An investigation of the effects of hard and soft errors on graphics processing unit-accelerated molecular dynamics simulations

2014 ◽  
Vol 26 (13) ◽  
pp. 2134-2140 ◽  
Author(s):  
Robin M. Betz ◽  
Nathan A. DeBardeleben ◽  
Ross C. Walker
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Graphics Processing Unit ◽  
Soft Errors ◽  
Processing Unit ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations ◽  
Graphics Processing

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 Accelerated Molecular Dynamics Simulations with the AMOEBA Polarizable Force Field on Graphics Processing Units

2013 ◽  
Vol 9 (11) ◽  
pp. 4684-4691 ◽  
Author(s):  
Steffen Lindert ◽  
Denis Bucher ◽  
Peter Eastman ◽  
Vijay Pande ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Molecular Dynamics Simulations ◽  
Graphics Processing Units ◽  
Polarizable Force Field ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations ◽  
Graphics Processing

scholarly journals Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations

2011 ◽  
Vol 8 (1) ◽  
pp. 17-23 ◽  
Author(s):  
William Sinko ◽  
César Augusto F. de Oliveira ◽  
Levi C. T. Pierce ◽  
J. Andrew McCammon
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Energy ◽  
Energy Barriers ◽  
Accelerated Molecular Dynamics ◽  
New Equation ◽  
Dynamics Simulations

scholarly journals Bayesian Refinement of Accelerated Molecular Dynamics Simulations for Interpreting SAXS Experiments

2017 ◽  
Vol 112 (3) ◽  
pp. 580a
Author(s):  
Samuel Bowerman ◽  
Amy Rice ◽  
Jeff Wereszczynski
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

Accelerated molecular dynamics simulations of interstitial clusters in pure and Al-doped MgO

2006 ◽  
Vol 250 (1-2) ◽  
pp. 12-16 ◽  
Author(s):  
B.P. Uberuaga ◽  
R. Smith ◽  
A.R. Cleave ◽  
R.W. Grimes ◽  
A.F. Voter ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Accelerated Molecular Dynamics ◽  
Dynamics Simulations

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
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