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  The Molecular Dynamics Module of NWChem - Design and Application in Protein Simulations

Straatsma, T., & Helms, V. (2000). The Molecular Dynamics Module of NWChem - Design and Application in Protein Simulations. In R. Esser (Ed.), Molecular Dynamics on Parallel Computers (pp. 70-82). Singapore: World Scientific.

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Item Permalink: https://hdl.handle.net/21.11116/0000-0008-A3D9-B Version Permalink: https://hdl.handle.net/21.11116/0000-0008-A3DA-A
Genre: Book Chapter

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 Creators:
Straatsma, T.P.1, Author
Helms, Volkhard2, Author           
Affiliations:
1High Performance Computational Chemistry Group, Environmental Molecular Sciences, Laboratory, Pacific Northwest National Laboratory, Richland, WA, USA, ou_persistent22              
2Max Planck Research Group of Theoretical Biophysics, Max Planck Institute of Biophysics, Max Planck Society, ou_2068294              

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 Abstract: NWChem is the massively parallel computational chemistry software package developed by the High Performance Computational Chemistry group for the Environmental Molecular Sciences Laboratory at the U.S. Department of Energy's Pacific Northwest National Laboratory. This software includes modules for quantum-mechanical and classical computational chemistry. This contribution details the implementation and performance of the molecular dynamics simulation module. The module is based on a domain decomposition approach to make it efficient for the simulation of large molecular systems on massively parallel computer architectures, despite the added complexity to deal with the necessary periodic atomic reassignments and dynamic load balancing techniques for heterogeneous systems. The calculation of atomic forces is the component that requires most of the communication and computational resources in molecular simulations. The use of the Global Array tools for one-sided asynchronous communication between processors allows this component to be carried out very efficiently when dynamic load balancing techniques are used.

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Language(s): eng - English
 Dates: 2000-02-01
 Publication Status: Issued
 Pages: 13
 Publishing info: -
 Table of Contents: -
 Rev. Type: Peer
 Identifiers: DOI: 10.1142/9789812793768_0004
 Degree: -

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Title: Molecular Dynamics on Parallel Computers
Source Genre: Book
 Creator(s):
Esser, Rüdiger1, Editor
Grassberger, Peter1, Author
Grotendorst, Johannes1, Author
Lewerenz, Marius2, Author
Affiliations:
1 NIC, Research Centre Jülich, Germany, ou_persistent22            
2 Université Pierre et Marie Curie, France, ou_persistent22            
Publ. Info: Singapore : World Scientific
Pages: 392 Volume / Issue: - Sequence Number: - Start / End Page: 70 - 82 Identifier: DOI: 10.1142/4353
ISBN: 978-981-02-4232-9
ISBN: 978-981-4493-55-0