We regret to announce that the Very Large System Simulation workshop has been cancelled. Thanks to all who applied. We are planning to try again later in this year.

NIH-sponsored workshops on Theoretical and Computational Biophysics
University of Illinois at Urbana-Champaign

Very Large System Simulation Workshop

Structure of the HIV Capsid

Computational biology in the petascale era offers a unique opportunity to connect atomic-level descriptions of biological systems such as viruses and cellular organelles. The course will introduce participants to the many challenges that arise in the course of conducting molecular dynamics simulations on very large biomolecular complexes. Relevant physical concepts, mathematical techniques, and computational methods will be introduced, including approaches for preparing, simulating, and analyzing large systems on state-of-the-art petascale supercomputing hardware, data management practices, and remote visualization, using the NAMD and VMD software. The workshop will be presented by members of the Theoretical and Computational Biophysics Group from the University of Illinois at Urbana-Champaign.

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 molecular dynamics simulation of large biomolecular complexes on petascale computing systems. Theory and methodology 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. The workshop will make use of remote computational and visualization resources at national supercomputer centers. Familiarity with NAMD and VMD is required*. Enrollment limited to 26 participants. The workshop will be held August 11-15, 2014, in Urbana, Illinois. All participants are required to bring their own laptop for use in the workshop training sessions. Those interested must apply for and be accepted into the workshop. Participants must arrange and pay for their own travel. Registration fees and important dates are described below.

Computational Biophysics Workshops

August 11-15, 2014

Theoretical & Computational Biophysics Group
University of Illinois
Beckman Institute
405 N Mathews Ave
Urbana, IL 61801



K. Schulten (UIUC)
J. Stone (UIUC)
J. Phillips (UIUC)
J. Perilla (UIUC
D. Chandler (UIUC)
T. Rudack (UIUC)
R. McGreevy (UIUC)
B. C. Goh (UIUC)
K. Cassidy (UIUC)


General Questions:

* Familiarity with NAMD and VMD can be demonstrated through participation in a prior TCBG computational biophysics workshop, or by having completed the Using VMD tutorial and the NAMD Tutorial in detail.

Registration fee: $75; fee is non-refundable. Enrollment limited to 26 participants. Participants must arrange and pay for their own travel and housing. Housing provided at the Hampton Inn. More on travel to the Beckman Institute is available here.

Significant Dates
Date in 2014:
Application deadline for full consideration:
July 23, 8:00 am CST
Selection and notification of participants by:
Ongoing through July 25
Confirmation of attendance by participants due by:
Two days after acceptance notice
Payment of workshop fee due by:
Five business days after confirming attendance

The workshop will be held at the Beckman Institute on the UIUC campus and is sponsored by:
National Institute of General Medical Sciences
NIH Center for Macromolecular Modeling and Bioinformatics (NIH 9P41GM104601)
Last Updated: March 11, 2014
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