NIH-sponsored Workshops on Theoretical and Computational Biophysics
Beckman Institute, Urbana, IL
August 2-4, 2013

Workshop on GPU Programming for Molecular Modeling

GPU Programming

Note: Basic familiarity with CUDA is assumed for this workshop. Participants are also encouraged to attend the multi-site "Proven Algorithmic Techniques for Many-core Processors" summer school the preceding week (July 29 - August 2) at the location of their choice.

The GPU Programming for Molecular Modeling workshop will extend GPU programming techniques to the field of molecular modeling, including subjects such as particle-grid algorithms (electrostatics, molecular surfaces, density maps, and molecular orbitals), particle-particle algorithms with an emphasis on non-bonded force calculations, radial distribution functions in GPU histogramming, single-node multi-GPU algorithms, and GPU clusters. Specific examples utilizing the NAMD and VMD software programs will be introduced and discussed in detail. Participants are invited and encouraged to bring their own molecular modeling problems to the workshop, for group discussion of how to address those problems via accelerated GPU hardware.

The workshop is designed for researchers in computational and/or biophysical fields who seek to extend their GPU programming skills to include molecular modeling. Advanced lecture sessions will be followed by extended discussion periods between lecturers and participants and laboratory time in which students will be able to work on their own molecular modeling GPU codes. Enrollment is limited to 20 participants; application deadline is July 15, selection and notification of participants is ongoing through July 17, 2013. The workshop will be held August 2-4, 2013, in Urbana, Illinois. All participants are required to bring their own laptop, for use in the workshop training sessions. Participants must arrange and pay for their own travel and accommodations.

Computational Biophysics Workshops

August 2-4, 2013

Beckman Institute for Advanced Science and Technology
405 N. Mathews Avenue
Urbana, IL



Fernanda Foertter (OLCF)
Mike Hallock (UIUC)
David Hardy (UIUC)
Joseph Peterson (UIUC)
Jim Phillips(UIUC)
John Stone (UIUC)
Ivan Ufimtsev (Stanford)

Kirby Vandivort (UIUC)



Registration fee: $50; fee is non-refundable. Enrollment limited to 20 participants.  Participants must arrange and pay for their own travel and accommodations. See here for local housing options. Please contact with any questions or comments.

Significant Dates
Date (in 2013):
Application deadline for full consideration:
July 15
Selection and notification of participants by:
Ongoing through July 17
Confirmation of attendance by participants due by:
Two days after acceptance notice
Payment of workshop fee due by:
Five business days after confirmation

The workshop will be held at the Beckman Institute for Advanced Science and Technology on the University of Illinois at Urbana-Champaign campus and is sponsored by:
National Institute of General Medical Sciences
NIH Center for Macromolecular Modeling and Bioinformatics (NIH P41-RR005969)
Workshop advertised in part via the Computational Chemisty List (
Last updated: June 6, 2013
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