61st Hands-on Workshop on Computational Biophysics

Auburn University, June 24-28, 2024

Register for Free

Join us this summer at Auburn University for the 61st Hands-On Workshop on Computational Biophysics, presented by the NIH Center for Macromolecular Modeling & Visualization of the University of Illinois at Urbana-Champaign

Dive into the world of computational biophysics through state-of-the-art techniques and tools in this comprehensive workshop. Our expert members from the NIH Center will guide you through a range of topics, including:

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Molecular Dynamics Simulations

Learn the fundamentals and advanced applications using NAMD. Get to know about NAMD 3.0 and the new advancements in GPU-computing with the software developers. 

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Biomolecular Visualization and Analysis

Gain hands-on experience with VMD. Have direct access to the software developers from UIUC, Auburn University and NVIDIA. You will be the first to try our new VMD 2.0, with completely modernized interface. 

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Nanotechnology Simulations

Explore new simulation techniques with ARBD. Learn how to simulate very large systems using Brownian Dynamics. Get to know the software developers and have a hands-on interaction with the software. 

How to participate

1

Apply for free here

For full consideration apply by May 15, 2024
Space is limited to 35 participants!
2

Get accepted

Notification of the participants will be done by May 17, 2024.  
3

Confirm your attendance

Confirm your attendance by May 24, 2024. 

This workshop is perfect for students and researchers from computational and biophysical backgrounds. It's also highly beneficial for experimentalists and non-specialists, thanks to QwikMD, an innovative teaching tool that simplifies the learning process by integrating NAMD and VMD.

Morning Sessions

Experts on biomolecular simulation will introduce the core theories and concepts in a clear and engaging manner.

Afternoon Sessions

Apply what you've learned in guided tutorials using NAMD, VMD, QwikMD, ARDB, and Cybershuttle.

Program

9:00 - Opening Remarks  (Emad Tajkhorshid)


9:30 - Applications of Molecular Dynamics to Biomolecular Modeling (Emad Tajkhorshid) Recording


10:30 - Coffee Break


10:45 - Introduction to VMD 2.0 (Diego Gomes) Recording


11:15 - Introduction to NAMD 3.0 (David Hardy / Rafael Bernardi) Recording -- Slides


11:45 - Molecular Dynamics: Setup and Analysis with QwikMD (Rafael Bernardi) Recording -- Slides


12:15 - Q & A


12:30 - Lunch Break (The Edge at Central Dining)


14:00 - Hands-on tutorial session day 1


15:30 - Coffee Break


17:00 - Adjourn for the day. 

9:00 - Enhanced Sampling and Free Energy Calculations in NAMD – part I (Chris Chipot) Recording

10:30 - Coffee Break

10:45 - Enhanced Sampling and Free Energy Calculations in NAMD – part II (Chris Chipot) Recording

11:15 - Collective Variables in NAMD (Jérôme Henin & Giacomo Fiorin) Recording -- Slides

12:15 - Q & A

12:30 - Lunch Break (The Edge at Central Dining)

14:00 - Hands-on tutorial session day 2

15:30 - Coffee Break

17:00 - Adjourn for the day. 

9:00 - Force Field Parameterization in Molecular Dynamics simulations (JC Gumbart) Recording -- Slides

10:30 - Coffee Break

10:45 - Force Field Parameterization with FFTK (JC Gumbart) Recording

11:15 - NAMD 3.0 Features, Performance and Capabilities (David Hardy / Eric Bohm / Haochuan Chen) Recording -- Slides(Part2) -- Slides(Part3)

12:15 - Q & A

12:30 - Lunch Break (The Edge at Central Dining)

14:00 - Hands-on tutorial session day 3

15:30 - Coffee Break

17:00 - Adjourn for the day. 

9:00 - Molecular Dynamics in the Era of Exascale Computing (Rafael Bernardi) Recording -- Slides

10:30 - Advanced Analysis Methods: Network Analysis (Marcelo Melo) Recording

10:30 - Coffee Break

10:45 - VMD 2.0 Features, Performance and Capabilities (John Stone) Recording

12:00 - How to Produce High-Quality Images with VMD (Diego Gomes) Recording

12:15 - Q & A

12:30 - Lunch Break (The Edge at Central Dining)

14:00 - Hands-on tutorial session day 4

15:30 - Coffee Break

17:00 - Adjourn for the day. 

9:00 - Coarse-Grained Simulation of Biological and Biotechnological Systems (Chris Maffeo) Recording -- Slides

9:45 - Deciphering Sequence-Dependent DNA Properties Using MD Simulations (Hemani Chhabra) Recording

10:30 - Coffee Break

10:45 - Introduction to Cybershuttle (Suresh Marru) Recording

11:15 - Cybershuttle for Protein Modeling (Diego Gomes) Recording

11:45 - Cybershuttle for Molecular Dynamics Applications (Sudhakar Pamidighantam) Recording

12:15 - Q & A

12:30 - Lunch Break (The Edge at Central Dining)

14:00 - Hands-on tutorial session day 5

15:30 - Coffee Break

17:00 - End of the Workshop. 

Instructors

Emad Tajkhorshid
University of Illinois at Urbana-Champaign

Rafael C. Bernardi
Auburn University

David Hardy
University of Illinois at Urbana-Champaign

John Stone
NVIDIA

Eric Bohm
University of Illinois at Urbana-Champaign

Diego E. B. Gomes
Auburn University

Haochuan Chen
University of Illinois at Urbana-Champaign

Jérôme Henin
CNRS, France

JC Gumbart
Georgia Institute of Technology

Giacomo Fiorin
National Institutes of Health

Chris Chipot
CNRS, France
The workshop will be in person, organized by the University of Illinois at Urbana-Champaign and Auburn University, and is sponsored by:


National Institute of General Medical Sciences
NIH Resource for Macromolecular Modeling and Visualization (NIH R24-GM145965)

Computational resources provided by ACCESS
National Center for Supercomputing Applications at the University of Illinois

This Workshop advertised in part via a posting to the Computational Chemistry List (CCL.net)

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