Biomedical Applications of Molecular Dynamics on the TeraGrid

April 17-19, 2002

NCSA Site: http://www.ncsa.uiuc.edu/Divisions/eot/Training/NAMD/

Pictures from the Workshop

Evaluation Results ( 185k PDF)

Principal Instructors: Klaus Schulten, Jim Phillips, Justin Gullingsrud

Additional Presenters: Bruce Loftis (NCSA), Mu Gao, Emad Tajkhorshid, Barry Isralewitz

Access Grid Sites

• Boston University: http://scv.bu.edu/accessgrid/
• Ohio Supercomputing Center: http://oscinfo.osc.edu/notices/r1013182813.html
• North Dakota State University: http://www.ndsu.nodak.edu/accessgrid/
• Pittsburgh Supercomputing Center: http://www.psc.edu/training/namd/namd.html
• Purdue University: http://www-rcd.cc.purdue.edu/events/NAMD.html

Recommended Readings

NAMD User's Guide (online or 408k PDF)

NAMD Release Notes (online)

Algorithmic challenges in computational molecular biophysics. Tamar Schlick, Robert Skeel, Axel Brünger, Laxmikant Kalé, John A. Board Jr., Jan Hermans, and Klaus Schulten. Journal of Computational Physics, 151:9-48, 1999.

NAMD2: Greater scalability for parallel molecular dynamics. Laxmikant Kalé, Robert Skeel, Milind Bhandarkar, Robert Brunner, Attila Gursoy, Neal Krawetz, James Phillips, Aritomo Shinozaki, Krishnan Varadarajan, and Klaus Schulten. Journal of Computational Physics, 151:283-312, 1999.

Steered molecular dynamics investigations of protein function. Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Journal of Molecular Graphics and Modeling, 19:13-25, 2001. Also in Protein Flexibility and Folding, L. A. Kuhn and M. F. Thorpe, editors, Biological Modeling Series (Elsevier).

Steered molecular dynamics and mechanical functions of proteins. Barry Isralewitz, Mu Gao, and Klaus Schulten. Current Opinion in Structural Biology, 11:224-230, 2001.

Molecular dynamics study of bacteriorhodopsin and the purple membrane. Jerome Baudry, Emad Tajkhorshid, Ferenc Molnar, James Phillips, and Klaus Schulten. Journal of Physical Chemistry B, 105:905-918, 2001.

All-atom emperical potential for molecular modeling and dynamics studies of proteins. MacKerell, A., et al. J. Phys. Chem. B., 102:3586-3616, 1998.

Agenda

Software for Hands-On

VMD 1.7.1 (not 1.7.2) installed on your desktop workstation or PC.

Configure your browser to use VMD (optional)

BioCoRE running in a browser on your desktop, with an account for the workshop project (register for an account, then email jim@ks.uiuc.edu with your login to be added to this project).

NAMD 2.5b1 (announcement, notes, docs) at NCSA (installed on Origin) or some other resource, possibly on your desk.

Hands-On Materials

Building Gramacidin A