Auburn University, June 24-28, 2024
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
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.
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.
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
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.
Experts on biomolecular simulation will introduce the core theories and concepts in a clear and engaging manner.
Apply what you've learned in guided tutorials using NAMD, VMD, QwikMD, ARDB, and Cybershuttle.
9:00 - Opening Remarks (Emad Tajkhorshid)
9:30 - Applications of Molecular Dynamics to Biomolecular Modeling (Emad Tajkhorshid)
10:30 - Coffee Break
10:45 - Introduction to VMD 2.0 (Diego Gomes)
11:15 - Introduction to NAMD 3.0 (David Hardy / Rafael Bernardi)
11:45 - Molecular Dynamics: Setup and Analysis with QwikMD (Rafael Bernardi)
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)
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 (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)
10:30 - Coffee Break
10:45 - Force Field Parameterization with FFTK (JC Gumbart)
11:15 - NAMD 3.0 Features, Performance and Capabilities (David Hardy / Eric Bohm / Haochuan Chen)
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)
10:30 - Advanced Analysis Methods: Network Analysis (Marcelo Melo)
10:30 - Coffee Break
10:45 - 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 (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)
9:45 - Deciphering Sequence-Dependent DNA Properties Using MD Simulations (Hemani Chhabra)
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 (The Edge at Central Dining)
14:00 - Hands-on tutorial session day 5
15:30 - Coffee Break
17:00 - End of the Workshop.
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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