A VMD plugin for NAMD simulations on Amazon EC2

Procedia Computer Science

Volumn 9, Issue , 2012, Pages 136-145

  Wong, Adam K L ^a   Goscinski, Andrzej M ^a  

^a DEAKIN UNIVERSITY   (Australia)

Author keywords

Amazon EC2; Cloud; High performance computing; Molecular dynamics simulation; NAMD; VMD

Indexed keywords

EID: 84896906300     PISSN: 18770509     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1016/j.procs.2012.04.015     Document Type: Conference Paper

References (22)

1. Amazon Elastic Compute Cloud (Amazon EC2). http://aws.amazon.com/ec2. Last access: August 2011.
2. Amazon Web Service (AWS) Management Console. http://aws.amazon.com/ console. Last access: August 2011.
3. M. Bhandarkar et al. "NAMD User Guide Version 2.8,", Theoretical Biophysics Group University of Illinois and Beckman Institute. 2011.
4. Charm++. http://charm.cs.uiuc.edu. Last access: August 2011.
5. Computer-Aided Drug Design Center, School of Pharmacy, University of Maryland. http://mackerell.umaryland.edu/CADD/CADD-center.html. Last access: August 2011.
6. Curl. http://curl.haxx.se. Last access: August 2011.
7. P. L. Freddolino, A. S. Arkhipov, S. B. Larson, A. McPherson, and K. Schulten. "Molecular dynamics simulations of the complete satellite tobacco mosaic virus,", Structure, 14:437-449, 2006.
8. A. Goscinski, M. Brock and P. Church. "High Performance Computing Clouds. Cloud computing: methodology, system, and applications,", CRC, Taylor & Francis group. 2011.
9. Interactive Molecular Dynamics Simulation. http://www.ks.uiuc.edu/ Research/vmd/imd. Last access: August 2011.
10. A. McPherson. Department of Biological Sciences, Molecular Biology and Biochemistry, University of California, Irvine. http://darwin.bio.uci.edu/ ~faculty/mcpherson. Last access: August 2011.
11. NAMD Molecular Dynamics Simulator. http://www.ks.uiuc.edu/Research/namd. Last access: August 2011.
12. Protein Data Bank. http://www.pdb.org. Last access: August 2011.
13. J. K.R. Ramakrishnan, L. M. K. Canon, S. Cholia, S. Shalf, H.J. Wasserman and N.J. Wright. "Performance Analysis of High Performance Computing Applications on the Amazon Web Services Cloud,", In Proceedings of IEEE Second International Conference in Cloud Computing Technology and Science (CloudCom), pp. 159-68, 2010.
14. Satellite Tobacco Mosaic Virus. http://www.ks.uiuc.edu/Research/STMV. Last access: August 2011.
15. Simple Command-Line Access to Amazon EC2. http://aws.amazon.com/ developertools/739. Last access: August 2011.
16. STMV simulation source. http://www.ks.uiuc.edu/Research/namd/utilities. Last access: August 2011.
17. Theoretical and Computational Biophysics Group at the Beckman Institute of the University of Illinois at Urbana-Champaign. http://www.ks.uiuc.edu/ Overview/People. Last access: August 2011.
18. The MPI Forum. http://www.mpi-forum.org. Last access: August 2011.
19. The Perl Programming Language. http://www.perl.org. Last access: August 2011.
20. VMD Molecular Graphics Viewer. http://www.ks.uiuc.edu/Research/vmd. Last access: August 2011.
21. VMD Plugin Library. http://www.ks.uiuc.edu/Research/vmd/plugins. Last access: August 2011.
22. B. Welch, K. Jones and J. Hobbs. "Practical Programming in Tel and Tk,", Prentice Hall, Upper Saddle River, NJ, USA, 2003.