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.

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.

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 GPU-accelerated alignment of bisulfite-treated short-read sequences

2017 ◽  
Author(s):  
Richard Wilton ◽  
Xin Li ◽  
Andrew P. Feinberg ◽  
Alexander S. Szalay
Keyword(s):  
Dna Sequences ◽  
Graphics Processing Unit ◽  
General Purpose ◽  
Processing Unit ◽  
Short Read ◽  
Wide Range ◽  
Programming Logic ◽  
Short Read Aligner ◽  
Graphics Processing ◽  
Better Than

AbstractThe alignment of bisulfite-treated DNA sequences (BS-seq reads) to a large genome involves a significant computational burden beyond that required to align non-bisulfite-treated reads. In the analysis of BS-seq data, this can present an important performance bottleneck that can potentially be addressed by appropriate software-engineering and algorithmic improvements. One strategy is to integrate this additional programming logic into the read-alignment implementation in a way that the software becomes amenable to optimizations that lead to both higher speed and greater sensitivity than can be achieved without this integration.We have evaluated this approach using Arioc, a short-read aligner that uses GPU (general-purpose graphics processing unit) hardware to accelerate computationally-expensive programming logic. We integrated the BS-seq computational logic into both GPU and CPU code throughout the Arioc implementation. We then carried out a read-by-read comparison of Arioc's reported alignments with the alignments reported by the most widely used BS-seq read aligners. With simulated reads, Arioc's accuracy is equal to or better than the other read aligners we evaluated. With human sequencing reads, Arioc's throughput is at least 10 times faster than existing BS-seq aligners across a wide range of sensitivity settings.The Arioc software is available at https://github.com/RWilton/Arioc. It is released under a BSD open-source license.

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 On the Performance and Energy Consumption of Molecular Dynamics Applications for Heterogeneous CPU-GPU Platforms Based on Gromacs

2017 ◽  
Vol 17 (5) ◽  
pp. 68-80
Author(s):  
Armen Poghosyan ◽  
Hrachya Astsatryan ◽  
Wahi Narsisian ◽  
Yevgeni Mamasakhlisov
Keyword(s):  
Molecular Dynamics ◽  
Energy Consumption ◽  
High Performance ◽  
Graphics Processing Unit ◽  
Large Data ◽  
Data Sets ◽  
Processing Unit ◽  
Many Body Systems ◽  
The Stability ◽  
Dynamics Simulations

Abstract High Performance Computing (HPC) accelerates life science discoveries by enabling scientists to analyze large data sets, to develop detailed models of entire biological systems and to simulate complex biological processes. As computational experiments, molecular dynamics simulations are widely used in life sciences to evaluate the equilibrium nature of classical many-body systems The modelling and molecular dynamics study of surfactant, polymer solutions and the stability of proteins and nucleic acids under different conditions, as well as deoxyribonucleic acid proteins are studied. The study aims to understand the scaling behavior of Gromacs (Groningen machine for chemical simulations) on various platforms, and the maximum performance in the prospect of energy consumption that can be accomplished by tuning the hardware and software parameters. Different system sizes (48K, 64K, and 272K) from scientific investigations have been studied show that the GPU (Graphics Processing Unit) scales rather beneficial than other resources, i.e., with GPU support. We track 2-3 times speedup compared to the latest multi-core CPUs. However, the so-called “threading effect” leads to the better results.

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