scholarly journals Frontiers in High-Performance, Large-Scale Molecular Dynamics. 35 Years of Molecular-Dynamics Simulations of Biological Systems

2013 ◽  
Vol 71 (2) ◽  
pp. 159 ◽  
Author(s):  
Wensheng Cai ◽  
Chipot Christophe
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Performance ◽  
Large Scale ◽  
Biological Systems ◽  
Dynamics Simulations

scholarly journals Enabling the execution of large scale workflows for molecular dynamics simulations

2021 ◽  
Author(s):  
Pau Andrio ◽  
Adam Hospital ◽  
Cristian Ramon-Cortes ◽  
Javier Conejero ◽  
Daniele Lezzi ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
High Performance ◽  
Large Scale ◽  
Workflow Management ◽  
Building Blocks ◽  
Data Dependencies ◽  
Computer Scientists ◽  
Computing Platforms ◽  
Dynamics Simulations

AbstractThe usage of workflows has led to progress in many fields of science, where the need to process large amounts of data is coupled with difficulty in accessing and efficiently using High Performance Computing platforms. On the one hand, scientists are focused on their problem and concerned with how to process their data. On top of that, the applications typically have different parts and use different tools for each part, thus complicating the distribution and the reproducibility of the simulations. On the other hand, computer scientists concentrate on how to develop frameworks for the deployment of workflows on HPC or HTC resources; often providing separate solutions for the computational aspects and the data analytic ones.In this paper we present an approach to support biomolecular researchers in the development of complex workflows that i) allow them to compose pipelines of individual simulations built from different tools and interconnected by data dependencies, ii) run them seamlessly on different computational platforms, and iii) scale them up to the large number of cores provided by modern supercomputing infrastructures. Our approach is based on the orchestration of computational building blocks for Molecular Dynamics simulations through an efficient workflow management system that has already been adopted in many scientific fields to run applications on multitudes of computing backends.Results demonstrate the validity of the proposed solution through the execution of massively parallel runs in a supercomputer facility.

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 Bimodal Grain-Size Scaling of Thermal Transport in Polycrystalline Graphene from Large-Scale Molecular Dynamics Simulations

Nano Letters ◽  
2017 ◽  
Vol 17 (10) ◽  
pp. 5919-5924 ◽  
Author(s):  
Zheyong Fan ◽  
Petri Hirvonen ◽  
Luiz Felipe C. Pereira ◽  
Mikko M. Ervasti ◽  
Ken R. Elder ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Grain Size ◽  
Molecular Dynamics Simulations ◽  
Thermal Transport ◽  
Large Scale ◽  
Size Scaling ◽  
Dynamics Simulations ◽  
Bimodal Grain Size

Large-scale molecular dynamics simulations of nanomachining

2017 ◽  
pp. 141-177 ◽  
Author(s):  
Stefan J. Eder ◽  
Ulrike Cihak-Bayr ◽  
Davide Bianchi
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Large Scale ◽  
Dynamics Simulations
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