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

Recommended Readings

NAMD User's Guide (online or 1.1M 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

Wednesday, April 17
   
Morning Location: E102 SRP

8:30 Breakfast and check-in  
9:00 Welcome  
9:15 Overview of NCSA Computational Resources Bruce Loftis
10:00 Break  
10:15 Introduction to Molecular Dynamics Simulations Klaus Schulten
11:00 What Can We Learn from MD Simulations? Klaus Schulten
11:45 - 1:00 Lunch  
     
Afternoon Location: E102 SRP  

1:00 Case Study: Unfolding the Muscle Protein Titin Mu Gao
1:45 Case Study: Aquaporin Membrane Channels Emad Tajkhorshid
2:30 Break  
2:45 Case Study: ATP Synthase Stalk Rotation Barry Isralewitz
3:30 Overview of Applicable Hardware and Software Jim Phillips
4:15 - 5:00 Discussion, Q and A Klaus Schulten
Evaluation Form (Wednesday and Thursday on separate pages)
     
Thursday, April 18
   
Morning Location: E102 SRP

8:30 Breakfast  
9:00 Configuring and Running NAMD Simulations Jim Phillips
9:30 Building Molecular Structures for NAMD Justin Gullingsrud
10:00 Break  
10:15 Assembling Molecular Systems for NAMD Justin Gullingsrud
11:00 Integrating the Equations of Motion Jim Phillips
11:45 - 1:00 Lunch  
     
Afternoon Location: E102 SRP  

1:00 Accelerating Processes via Steered MD Klaus Schulten
1:45 Analysis of MD Trajectories Justin Gullingsrud
2:30 Break  
2:45 Efficient Evaluation of Forces Jim Phillips
3:30 NAMD Serial and Parallel Performance Jim Phillips
4:15 - 5:00 Discussion, Q and A Klaus Schulten
Evaluation Form (Wednesday and Thursday on separate pages)
     
Friday, April 19
     
Morning Location: 3414 Beckman Institute  

Optional Hands-On Session, Instructors Available
8:30 Breakfast (on your own in Beckman atrium cafe for coffee, bagels, etc., no food allowed in 3414)  
9:00 Hands-On: Assembly of Gramicidin in a Membrane Jim Phillips & Justin Gullingsrud
10:00 Break (Beckman atrium)  
10:15 - 12:00 Hands-On: Equilibration of Gramicidin in a Membrane Jim Phillips & Justin Gullingsrud
Evaluation Form (Friday)
     

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

VMD scripts have access to the full power of the Tcl scripting language, which includes deleting, modifying, or distributing your files! Do not run scripts from people you do not know or trust.

Building Gramacidin A