63rd Hands-on Workshop on Computational Biophysics

Auburn University, August 4-8, 2025

Register for Free

Join us this Summer at Auburn University for the 63rd Hands-On Workshop on Computational Biophysics, presented by the NIH Resource for Macromolecular Modeling & Visualization of the University of Illinois 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 resource will guide you through a range of topics, including:

Mobirise

Molecular Dynamics Simulations

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

Mobirise

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 try our new VMD 2.0, with a completely modernized interface.

How to participate

1

Apply for free here

For full consideration apply by 11:59 PM CST June 20, 2025
Space is limited to 35 participants!
2

Get accepted

Notification of the participants will be done by June 27, 2025.  
3

Confirm your attendance

Confirm your attendance by July 4, 2025. 

This workshop is ideal 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)

10:00 - Introduction to NAMD, VMD, and QwikMD (Rafael Bernardi)

10:30 - Coffee Break

10:45 - Fundaments of Molecular Dynamics Simulations (Rafael Bernardi)

12:00 - Guidelines to use the tutorials (JC Gumbart)

12:20 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on Tutorials, Day 1 **

15:30 - Coffee Break

17:00 - Adjourn for the Day

* Lunch will be provided

** Recommended Tutorials: VMD Tutorial; NAMD Tutorial

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

10:00 - Force Field Parameterization with FFTK (JC Gumbart)

10:45 - Coffee Break

11:00 - Flash Talks - (Optional Participants Presentations)

12:30 - Lunch Break*

14:00 - Hands-on Tutorials, Day 2 ***

15:30 - Coffee Break

17:00 - Adjourn for the Day

18:00 - Workshop Dinner**

* Lunch will be provided

** Free for workshop participants

*** Recommended Tutorials: Parameterizing a Novel Residue Tutorial; Topology File Tutorial

9:00 - Introduction to Cybershuttle (Suresh Marru)

9:30 - Cybershuttle for Protein Modeling (Diego Gomes)

10:00 - Advanced Analysis Tools: Network Analysis (TBD)

10:30 - Coffee Break

10:45 - VMD 2.0 Features, Performance and Capabilities (Diego Gomes)

11:30 - How to Produce High-Quality Images with VMD (Diego Gomes)

12:00 - Meet the Developers (NAMD & VMD Developers)

12:20 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on Tutorials, Day 3 **

15:30 - Coffee Break

17:00 - Adjourn for the Day

* Lunch will be provided

** Recommended Tutorials: Cybershuttle Tutorial; Network Analysis Tutorial

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

10:30 - Coffee Break

10:45 - Enhanced Sampling and Free Energy Calculations in NAMD (TBD)

11:45 - Collective Variables in NAMD (Jérôme Henin & Giacomo Fiorin)

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on Tutorials, Day 4 **

15:30 - Coffee Break

17:00 - Adjourn for the Day

* Lunch will be provided

** Recommended Tutorials: Free Energy Tutorial; Adaptive Biasing Force Tutorial; Membrane Proteins Tutorial

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

10:30 - Coffee Break

10:45 - Molecular Dynamics in the Era of Exascale Computing (Priscila Gomes)

11:15 - Principles of Molecular Dynamics Flexible Fitting - MDFF (TBD)

12:15 - Q & A

12:30 - Lunch Break*

14:00 - Hands-on Tutorials, Day 5 **

15:30 - Coffee Break

17:00 - End of the Workshop

* Lunch will be provided

** Recommended Tutorials: QM/MM Tutorial; MDFF Tutorial

Instructors

Emad Tajkhorshid
University of Illinois Urbana-Champaign

Rafael C. Bernardi
Auburn University

Jérôme Henin
CNRS, France

David Hardy
University of Illinois Urbana-Champaign

John Stone
NVIDIA

Diego E. B. Gomes
Auburn University

Giacomo Fiorin
National Institutes of Health

Marcelo C. R. Melo

Colorado State University

Suresh Marru

Georgia Institute of Technology

Priscila Gomes

Auburn University

JC Gumbart
Georgia Institute of Technology

Where: In person at the Leach Science Center of the Auburn University

The workshop will be in person only, organized by the University of Illinois 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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