UNICORE-An Uniform Platform for Chemistry on the Grid

Journal of Computational Methods in Sciences and Engineering

Volumn 2, Issue 3-4, 2002, Pages 369-375

  Pytliński, Jaroslaw ^a   Skorwider, Lukasz ^a   Huber, Valentina ^b   Wroński, Michał ^c   Bała, Piotr ^c  

^a UNIVERSITY OF WARSAW   (Poland)

^b FORSCHUNGSZENTRUM JÜLICH   (Germany)

^c NICOLAUS COPERNICUS UNIVERSITY   (Poland)

Author keywords

Car Parrinello molecular dynamics; Grid computing; molecular dynamics; quantum chemistry

Indexed keywords

MOLECULAR DYNAMICS; QUANTUM CHEMISTRY; USER INTERFACES;

AS INTERFACES; BIO-MOLECULAR; CAR-PARRINELLO MOLECULAR-DYNAMICS; CONTROL MECHANISM; GRID TOOLS; JOB SUBMISSION; PLUG-INS; PROTEIN DATA BANK;

GRID COMPUTING;

EID: 1642319857     PISSN: 14727978     EISSN: None     Source Type: Journal    
DOI: 10.3233/JCM-2002-23-410     Document Type: Article

References (14)

1. C. Kesselman I. Foster, editor. The Grid: Blueprint for a Future Computing Infrastructure. Morgan Kaufman Publishers, USA, 1999.
2. Webmo. http://www.webmo.net.
3. M. J. Frisch, G. W. Trucks, H. B. Schlegel, G. E. Scuseria, M. A. Robb, J. R. Cheeseman, V. G. Zakrzewski, J. A. Montgomery, Jr., R. E. Stratmann, J. C. Burant, S. Dapprich, J. M. Millam, A. D. Daniels, K. N. Kudin, M. C. Strain, O. Farkas, J. Tomasi, V. Barone, M. Cossi, R. Cammi, B. Mennucci, C. Pomelli, C. Adamo, S. Clifford, J. Ochterski, G. A. Petersson, P. Y. Ayala, Q. Cui, K. Morokuma, P. Salvador, J. J. Dannenberg, D. K. Malick, A. D. Rabuck, K. Raghavachari, J. B. Foresman, J. Cioslowski, J. V. Ortiz, A. G. Baboul, B. B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R. Gomperts, R. L. Martin, D. J. Fox, T. Keith, M. A. Al-Laham, C. Y. Peng, A. Nanayakkara, M. Challacombe, P. M. W. Gill, B. Johnson, W. Chen, M. W. Wong, J. L. Andres, C. Gonzalez, M. Head-Gordon, E. S. Replogle, and J. A. Pople. Gaussian 98. 2001.
4. M. W. Schmidt, K. K. Baldridge, J. A. Boatz, M. S. Gordon S. T. Elbert, J. H. Jensen, S. Koseki, N. Matsunaga, K. A. Nguyen, S. J. Su, T. L. Windus, M. Dupuis, and J. A. Montgomery. General atomic and molecular electronic structure system. J. Comput. Chem. 14, 1347-1363, 1993.
5. J. J. P. Stewart, L. P. Davis, and L. W. Burggraf. Semi-empirical calculations of molecular trajectories: method and applications to some simple molecular systems. J. Comp. Chem. 8(8), 117 23. 1987.
6. M. Bhandarkar, G. Budescu, W. F. Humphrey, J. A. Izaguirre, S. Izrailev, L. V. Kal, D. Kosztin, F. Molnar, J. C. Phillips, and K. Schulten. Biocore: A collaboratory for structural biology. In A. G. Bruzzone, A. Uchrmacher, and E. H. Page, editors, Proceedings of the SCS International Conference on Web-Based Modeling and Simulation. San Francisco, California, 1999.
7. L. Kal, R. Skeel, M. Bhandarkar, R. Brunner, A. Gursoy, N. Krawetz, J. Phillips, A. Shinozaki, K. Varadarajan, and K. Schulten. Namd2: Greater scalability for parallel molecular dynamics. J. Comp. Phxjs. 151, 283-312, 1999.
8. UNICORE. Pallas. Germany, http://www.unicore.org.
9. W. Van Gunsteren and H. J. C. Berendsen. GROMOS (Groningen Molecular Simulation Computer Program Package). Biomos, Laboratory of Physical Chemistry, ETH Zentrum, Zurich, 1996.
10. P. Kollman. AMBER (Assisted Model Building with Energy Refinement). University of California, San Francisco, USA, 2001.
11. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus. A program for macromolecular energy, minimization, and dynamics calculations. J. Comp. Chem. 4, 187-217, 1983.
12. V. Huber. Supporting car-parrinello molecular dynamics with unicore. In Computational Science ICCS - San Francisco, USA, Proceedings, Pt. 1, Volume 2073, pp. 560-567. Springer Verlag, 2001.
13. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov and P. E. Bourne. The Protein Data Bank. Nucleic Acids Research 28, 235-242, 2000.
14. EUROGRID. http://www.eurogrid.org