Computational Biophysics

November 28 - December 1, 2005


  • National Center for Research Resources
  • PSC's Biomedical Initiative. An NIH Resource Center
  • NIH Resource for Macromolecular Modeling and Bioinformatics


Pittsburgh Supercomputing Center (PSC)
Mellon Institute Building, Pittsburgh, PA

APPLICATION DEADLINE: October 24, 2005 -- Applications are no longer being accepted


The workshop will explore physical models and computational approaches used for the simulation of biological systems and the investigation of their function at an atomic level. The course will be based on case studies including the properties of membranes and membrane proteins, mechanisms of molecular motors, trafficking in the living cell through water and ion channels, and signaling pathways. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including force fields and algorithms used in molecular modeling, molecular dynamics simulations on parallel computers and steered molecular dynamics simulations.
The workshop is designed for graduate students and postdoctoral researchers in computational and/or biophysical fields who seek to extend their research skills to include computational and theoretical expertise, as well as other researchers interested in theoretical and computational biophysics. Theory sessions in the morning will be followed by hands-on computer labs in the afternoon in which students will be able to set up and run simulations.

Enrollment is limited.



Introduction to Protein Structure and Dynamics
Statistical Mechanics of Proteins
Parameters for Classical Force Fields
Simulating Membrane Channelsp


Mon, 11/28: Introduction to Protein Structure and Dynamics, K. Schulten
08:30-08:45 Workshop Registration
08:45-09:00 Opening Remarks -- Ralph Roskies
09:00-09:30 Overview of National Resource for Biomedical Supercomputing (NRBSC)
09:30-10:30 Molecular Graphics Perspective of Protein Structure and Function
10:30-10:50 Coffee Break
10:50-12:00 Molecular Dynamics Method
12:00-12:30 Daily Q & A
12:30-1:30 Lunch Break
1:30-1:45 Overview of Hands-on Sessions  
1:50-2:30 Molecular Graphics Tutorial
2:30-2:45 Coffee Break
2:45-5:00 Molecular Graphics Tutorial (continued)
Tue, 11/29: Statistical Mechanics of Proteins, K. Schulten
09:00-10:00 Molecular Dynamics with NAMD
10:00-11:00 Equilibrium Properties of Proteins
11:00-11:15 Coffee Break
11:15-12:15 Nonequilibrium Properties of Proteins
Daily Q & A
Group photo
12:30-1:30 Lunch Break
1:30-3:30 Molecular Dynamics Tutorial
3:30-3:45 Coffee Break
3:45-5:00 Molecular Dynamics Tutorial (continued)
Wed, 11/30: Parameters for Classical Force Fields, E. Tajkhorshid
09:00-10:00 Introduction to Classical Force Fields
10:00-11:00 Force Fields Parameterization
11:00-11:15 Coffee Break
11:15-12:15 Applications
12:15-12:30 Daily Q&A
12:30-1:30 Lunch Break
1:30-3:00 Paramaterizing a Novel Residue
3:00-3:15 Coffee Break
3:15-5:00 Topology File Tutorial
Thu, 12/1: Simulating Membrane Channels, E. Tajkhorshid
09:00-10:00 Transport in Membrane Chanels
10:00-10:30 Nanotubes
10:30-10:40 Daily Q&A
10:40-10:50 Coffee Break /Evaluations
10:50-12:30 Nanotubes/IMD
12:30-1:30 Lunch Break
1:30- Open tutorial work time

Dr. Klaus Schulten
3147 Beckman Institute
University of Illinois
405 N. Mathews
Urbana, IL 61801

Dr. Emad Tajkhorshid
3143 Beckman Institute
University of Illinois
405 N. Mathews
Urbana, IL 61801

Slides from a previous workshop can be reviewed at:

NAMD -- recipient of a 2002 Gordon Bell Award , is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. Based on Charm++ parallel objects, NAMD scales to hundreds of processors on high-end parallel platforms and tens of processors on commodity clusters using gigabit ethernet. NAMD is file-compatible with AMBER, CHARMM, and X-PLOR and is distributed free of charge with source code.

VMD -- is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code.

Financial Information
This workshop is funded by grants from the NIH National Center for Research Resources. These grants provide tuition, hotel, supercomputing time, and workshop materials for US academic participants.

ALL participants are responsible for paying their own travel expenses. Complimentary continental breakfasts and lunches will be provided the days of the workshop.

A few positions may be available for US government employees and corporate and industrial researchers. These participants are responsible for their own hotel accommodations.

Tuition for US government employees is $350 in advance to cover the workshop materials and supercomputing time. (Contract government employees, if they submit a letter from their department head explaining their status as a contract employee, will be considered an academic participant.)

Tuition for corporate and industrial participants is $975 in advance to cover the workshop materials and supercomputing time.

Group Photo (5 x 7) --8.3 MB
Group Photo (8 x 10) --16 MB