PSC NAMD Workshop 2001

Wed. Aug. 15 through Sat. Aug. 18, 2001

PSC Workshop Schedule

PSC NAMD Workshop Page

Handouts in PDF format (also available via links in schedule below)

PSC Contacts

Troy Wymorewymore@psc.edu412-268-8858
Nancy Blankensteinblankens@pscuxc.psc.edu

Instructors

  • Klaus Schulten
  • Jim Phillips
  • Ioan Kosztin
  • Justin Gullingsrud

Agenda

Afternoon, Wednesday, August 15
11:30-12:30    Lunch and check-in
12:30-12:45    Welcome (Troy Wymore)
12:45- 1:15    Biomed Overview (David Deerfield)
 1:15- 1:30    Participant Introductions
 1:30- 2:30    Introduction to PSC (Tom Maiden)
 2:30- 3:30    Break/Setting up accounts in CTC
 3:30- 5:00    Hands-On: Viewing Molecules with VMD (Justin)

Morning, Thursday, August 16
 9:00- 9:15    Welcoming Remarks and Introductions (All)
 9:15-10:00    Introduction to MD Simulations (Klaus)
10:00-10:15    Break
10:15-10:45    Semi empirical Force Fields and Their Limitations (Ioan)
10:45-11:15    Configuring and Running NAMD Simulations (Jim)
11:15-12:30    Hands-On: Simulation of BPTI at Different Temperatures (Klaus)

Afternoon, Thursday, August 16
 2:00- 2:45    What Can We Learn from MD Simulations? (Klaus)
 2:45- 3:15    Case Study: Protein-Membrane Simulation (Klaus)
 3:15- 3:30    Break
 3:30- 4:00    Analysis of MD results using Statistical Mechanics Methods (Ioan)
 4:00- 5:15    Hands-On: Analysis of BPTI Equilibrium Properties (Ioan)
 5:15- 5:30    Break
 5:30- 7:00    Optional Hands-On Session (All)

Morning, Friday, August 17
 9:00- 9:45    Integrating the Equations of Motion (Jim)
 9:45-10:15    Building Molecular Structures for NAMD (Jim)
10:15-10:45    Break
10:45-11:15    Assembling Molecular Systems for NAMD (Justin)
11:15-12:30    Hands-On: Assembly of Gramicidin in a Membrane (Justin)

Afternoon, Friday, August 17
 2:00- 2:30    Efficient Evaluation of Forces (Jim)
 2:30- 3:00    Analysis of MD Trajectories (Ioan)
 3:00- 3:30    Break
 3:30- 4:00    Case Study: Signalling Proteins (Ioan)
 4:00- 5:15    Hands-On: Equilibration of Gramicidin in a Membrane (Justin)

Morning, Saturday, August 18
 9:00- 9:30    NAMD Serial and Parallel Performance (Jim)
 9:30-10:15    Case Study: Steered MD Simulation (Justin)
10:15-10:30    Break
10:30-11:45    Question/Answer, Discussion, and Evaluation
11:45- 1:00    Lunch

Recommended Readings

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

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

Barry Isralewitz, Jerome Baudry, Justin Gullingsrud, Dorina Kosztin, and Klaus Schulten. Steered molecular dynamics investigations of protein function. 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). abstract

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

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

NAMD 2.3 User's Guide (online or 362K PDF)

NAMD 2.3 Release Notes (online)

Additional Suggested Readings

Andrew R. Leach, Molecular Modelling: Principles and Applications, Addison Wesley 1996. Ch. 3: Empirical Force Field Models, Ch .5: Computer Simulation Methods, and Ch .6: Molecular Dynamics Simulation Methods.