62nd Hands-on Workshop on Computational Biophysics

Auburn University, December 16-20, 2024

Register for Free

Join us this winter at Auburn University for the 62nd 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. 

How to participate

1

Apply for free here

For full consideration apply by November 1, 2024
Spaces are limited to 35 participants!
2

Get accepted

Notification of the participants will be done by November 5, 2024.  
3

Confirm your attendance

Confirm your attendance by November 10, 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

In the mornings, you will have lectures with experts on biomolecular simulation. They 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)

9:15 - Applications of Molecular Dynamics to Biomolecular Modeling (Emad Tajkhorshid)

10:30 - Coffee Break

10:45 - Introduction to Molecular Dynamics with NAMD, VMD, and QwikMD (Rafael Bernardi)

11:45 - What is new in VMD 2.0 (Diego Gomes)

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on tutorial session day 1

15:30 - Coffee Break

17:00 - Adjourn for the day

* Lunch will be provided

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

10:30 - Coffee Break

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

11:45 - NAMD 3.0 Features, Performance and Capabilities (David Hardy)

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on tutorial session day 2

15:30 - Coffee Break

17:00 - Adjourn for the day 

18:00 - Workshop Dinner**

* Lunch will be provided
** Free for workshop participants

9:00 - Simulations of Membranes and Membrane Proteins (Emad Tajkhorshid)

10:00 - Molecular Dynamics in the Era of Exascale Computing (Rafael Bernardi)

10:30 - Coffee Break

10:45 - Advanced Analysis Methods: Network Analysis (Marcelo Melo)

11:30 - VMD 2.0 Features, Performance and Capabilities (John Stone)

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

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on tutorial session day 3

15:30 - Coffee Break

17:00 - Adjourn for the day 

* Lunch will be provided

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

10:30 - Coffee Break

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

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

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on tutorial session day 3

15:30 - Coffee Break

17:00 - Adjourn for the day 

* Lunch will be provided

9:00 - Studying Enzymatic Reactions with NAMD QM/MM (Marcelo Melo)

10:30 - Coffee Break

10:45 - Introduction to Cybershuttle (Suresh Marru)

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

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

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on tutorial session day 5

15:30 - Coffee Break

17:00 - End of the Workshop 

* Lunch will be provided

Instructors

Emad Tajkhorshid
University of Illinois at Urbana-Champaign

Rafael C. Bernardi
Auburn University

JC Gumbart
Georgia Institute of Technology

Jérôme Henin
CNRS, France

David Hardy
University of Illinois at Urbana-Champaign

John Stone
NVIDIA

Diego E. B. Gomes
Auburn University

Sudhakar Pamidighantam

Georgia Institute of Technology

Giacomo Fiorin
National Institutes of Health

Marcelo C. R. Melo

Colorado State University

Suresh Marru

Georgia Institute of Technology

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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