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An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture

Brown,AH and Walsh,TR 2015, An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture, Computer Physics Communications, vol. 192, pp. 278-281, doi: 10.1016/j.cpc.2015.02.025.

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Title An improved TIGER2 implementation for NAMD suitable for the Blue Gene architecture
Author(s) Brown,AH
Walsh,TRORCID iD for Walsh,TR orcid.org/0000-0002-0233-9484
Journal name Computer Physics Communications
Volume number 192
Start page 278
End page 281
Total pages 4
Publisher Elsevier
Place of publication Amsterdam, Netherlands
Publication date 2015-07
ISSN 0010-4655
Keyword(s) BlueGene/Q
Molecular dynamics
NAMD
Replica-exchange molecular dynamics
TIGER2 method
Tool command language
Summary Here we present an improved implementation of the TIGER2 Replica Exchange Molecular Dynamics (REMD) method, using the replica exchange Application Programming Interface (API) found in contemporary versions of the NAMD Molecular Dynamics Package. The implementation takes the form of a TCL script which is used in conjunction with the standard configuration file. This implementation is validated against a previous TIGER2 implementation, as well as data reported for the original TIGER2 simulations. Our implementation is compatible with a range of architectures; crucially it enables the use of this wrapper with the BlueGene/Q architecture, in addition to the x86 architecture. Program summary: Program title: TIGER2-NAMD. Catalogue identifier: AEWC_v1_0. Program summary URL: http://cpc.cs.qub.ac.uk/summaries/AEWC_v1_0.html Program obtainable from: CPC Program Library, Queen's University, Belfast, N. Ireland. Licensing provisions: Standard CPC licence, http://cpc.cs.qub.ac.uk/licence/licence.html No. of lines in distributed program, including test data, etc.: 34151. No. of bytes in distributed program, including test data, etc.: 424217. Distribution format: tar.gz. Programming language: Tcl 8.5. Computer: x86 Clusters, BlueGene/Q, Workstations. Operating system: Linux, IBM Compute Node Kernel. Has the code been vectorised or parallelised?: Yes. MPI Parallelism. Classification: 3. External routines: NAMD 2.9 (http://www.ks.uiuc.edu/Research/namd/). Nature of problem: Replica Exchange Molecular Dynamics. Solution method: Each replica runs through multiple cycles of heating and cooling with exchanges between them being attempted. Running time: Typically 30 mins, up to an hour.
Language eng
DOI 10.1016/j.cpc.2015.02.025
Field of Research 030402 Biomolecular Modelling and Design
080306 Open Software
030704 Statistical Mechanics in Chemistry
Socio Economic Objective 970103 Expanding Knowledge in the Chemical Sciences
HERDC Research category C1 Refereed article in a scholarly journal
ERA Research output type C Journal article
Copyright notice ©2014, Elsevier
Persistent URL http://hdl.handle.net/10536/DRO/DU:30072535

Document type: Journal Article
Collection: Institute for Frontier Materials
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Created: Tue, 21 Apr 2015, 13:32:38 EST

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