scholarly journals Collision-induced dissociation of protonated uracil water clusters probed by molecular dynamics simulations

2021 ◽  
Author(s):  
Linjie Zheng ◽  
Jérôme Cuny ◽  
Sébastien Zamith ◽  
Jean-Marc L'Hermite ◽  
Mathias Rapacioli
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Present Article ◽  
Molecular Species ◽  
Water Clusters ◽  
Collision Induced Dissociation ◽  
Chemical Information ◽  
Theoretical Support ◽  
Dynamics Simulations

Collision-induced dissociation experiments of hydrated molecular species can provide a wealth of important information. However, they often need a theoretical support to extract chemical information. In the present article, in...

scholarly journals Optimizing the performance of reactive molecular dynamics simulations for many-core architectures

2018 ◽  
Vol 33 (2) ◽  
pp. 304-321 ◽  
Author(s):  
Hasan Metin Aktulga ◽  
Chris Knight ◽  
Paul Coffman ◽  
Kurt A O’Hearn ◽  
Tzu-Ray Shan ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Species ◽  
Trajectory Data ◽  
Reactive Molecular Dynamics ◽  
Species Analysis ◽  
Dynamics Simulations ◽  
Many Core ◽  
Molecular Species Analysis

Reactive molecular dynamics simulations are computationally demanding. Reaching spatial and temporal scales where interesting scientific phenomena can be observed requires efficient and scalable implementations on modern hardware. In this article, we focus on optimizing the performance of the widely used LAMMPS/ReaxC package for many-core architectures. As hybrid parallelism allows better leverage of the increasing on-node parallelism, we adopt thread parallelism in the construction of bonded and nonbonded lists and in the computation of complex ReaxFF interactions. To mitigate the I/O overheads due to large volumes of trajectory data produced and to save users the burden of post-processing, we also develop a novel in situ tool for molecular species analysis. We analyze the performance of the resulting ReaxC-OMP package on two different architectures: (i) Mira, an IBM Blue Gene/Q system and (ii) Cori-II, a Cray XC-40 sytem with Knights Landing processors. For Pentaerythritol tetranitrate (PETN) systems of sizes ranging from 32 thousand to 16.6 million particles, we observe speedups in the range of 1.5–4.5×. We observe sustained performance improvements for up to 262,144 cores (1,048,576 processes) of Mira and a weak scaling efficiency of 91.5% in large simulations containing 16.6 million particles. The in situ molecular species analysis tool incurs only insignificant overheads across various system sizes and runs configurations.

Molecular dynamics simulations of binary collisions between water clusters

1998 ◽  
Vol 29 ◽  
pp. S543-S544
Author(s):  
Marcus Svanberg ◽  
Liu Ming ◽  
Markovic´ Nikola ◽  
Jan B.C. Pettersson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Water Clusters ◽  
Binary Collisions ◽  
Dynamics Simulations

Local Structure and Work of Formation of Water Clusters Studied by Molecular Dynamics Simulations

1996 ◽  
Vol 180 (1) ◽  
pp. 86-97 ◽  
Author(s):  
Elena N. Brodskaya ◽  
Jan Christer Eriksson ◽  
Aatto Laaksonen ◽  
Anatoly I. Rusanov
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Water Clusters ◽  
Dynamics Simulations
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