A VMD plugin for NAMD simulations on Amazon EC2

Wong, Adam K. L. and Goscinski, Andrzej M. 2012, A VMD plugin for NAMD simulations on Amazon EC2, in ICCS 2012 : Empowering science through computing : Procedia Computer Science : Proceedings of the 12th Annual International conference on Computational Science, Elsevier, Amsterdam, The Netherlands, pp. 136-145, doi: 10.1016/j.procs.2012.04.015.

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Title A VMD plugin for NAMD simulations on Amazon EC2
Author(s) Wong, Adam K. L.
Goscinski, Andrzej M.
Conference name Computational Science. Conference (12th : 2012 : Omaha, Neb.)
Conference location Omaha, Neb.
Conference dates 4-6 Jun. 2012
Title of proceedings ICCS 2012 : Empowering science through computing : Procedia Computer Science : Proceedings of the 12th Annual International conference on Computational Science
Editor(s) Ali, Hesham
Shi, Yong
Khazanchi, Deepak
Lees, Michael
van Albada, G. Dick
Dongarra, Jack
Sloot, Peter M.A.
Publication date 2012
Conference series Computational Science. Conference
Start page 136
End page 145
Total pages 10
Publisher Elsevier
Place of publication Amsterdam, The Netherlands
Keyword(s) molecular dynamics simulation
high performance computing
Amazon EC2
Summary VMD and NAMD are two major molecular dynamics simulation software packages, which can work together for mining structural information of bio-molecules. Carrying out such molecular dynamics simulations can help researchers to understand the roles and functions of various bio-molecules in life science research. Recently, clouds have provided HPC clusters on demand that allow users to benefit from their flexibility, elasticity, and lower costs. Although cloud computing promises to provide seamless access to HPC clusters through the abstraction of services, which hide the details of the underlying software and hardware infrastructure, users without in depth computing knowledge are still forced to cope with many low level system and programming details. Therefore, we have designed and developed a software plugin of VMD, which can provide an integrated framework for NAMD to be executed on Amazon EC2. The proposed Amazon EC2 Plugin for VMD frees users from performing many tedious computing tasks such as launching, connecting and terminating Amazon EC2 compute instances; configuring a HPC cluster; and installing middleware and software applications before the system is readily available for any scientific investigation. This allows VMD/NAMD users to spend less time getting applications to work on HPC clusters but more time for bio-research.
Notes This conference paper was published in Procedia Computer Science, v.9 2012 p.136-145
ISSN 1877-0509
Language eng
DOI 10.1016/j.procs.2012.04.015
Field of Research 080501 Distributed and Grid Systems
Socio Economic Objective 890206 Internet Hosting Services (incl. Application Hosting Services)
HERDC Research category E1 Full written paper - refereed
Persistent URL http://hdl.handle.net/10536/DRO/DU:30049208

Document type: Conference Paper
Collection: School of Information Technology
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