NAMD Developer Workshop - Chicago, August 10 - 11, 2022
Program
- Talks at room W301 at the Gordon Center for Integrative Science, University of Chicago, 929 E 57th St.
- Parking available at Campus North Parking, 5501 S Ellis Ave.
- All sessions broadcasted through Zoom. See links below.
Wednesday, August 10: Day 1 Zoom webinar link
|
Time (CT)* |
Title |
Speaker |
| 08:30-09:00 | Breakfast |
|
| 09:00-09:20 | NAMD progress and plans |
David Hardy NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 09:20-09:40 | Advanced features development in NAMD |
Mohammad Soroush Barhaghi NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 09:40-10:00 | NAMD roadmap. Missing features and needed developments |
Chris Chipot NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:00-10:30 | Discussion | |
| 10:30-10:45 | Coffee Break | |
| 10:45-11:05 | Galvani potential offset and constant-pH simulations of membrane proteins |
Benoît Roux University of Chicago |
| 11:05-11:25 | Acccelerating hydration transition of ligand binding with confinement potential |
Wei Jiang Argonne National Lab |
| 11:25-11:45 | The future of QM/MM in NAMD |
Rafael Bernardi Auburn University |
| 11:45-12:05 | Beyond MDFF, integrating relative entropy forces in NAMD |
Josh Vermaas Michigan State University |
| 12:05-12:25 | Full scale simulations on a budget: Implementing shaped based coarse graining in NAMD3 |
Juan Perilla University of Delaware |
| 12:25-13:10 | Lunch Break | |
| 13:10-13:30 | Multi-resolution simulations with ARBD |
Alek Aksimentiev NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 13:30-13:50 | AMBERff at scale: Multimillion-atom simulations with AMBER force fields in NAMD |
Jodi Hadden-Perilla University of Delaware |
| 13:50-14:10 | FFTK updates |
JC Gumbart Georgia Institute of Technology |
| 14:10-15:00 | Discussion | |
| 15:00-15:15 | Coffee Break | |
| 15:15-15:35 | Learning electrostatic complementarity using inception networks and molecular models | Abhishek Singharoy Arizona State University |
| 15:35-15:55 | Intelligent steered molecular dynamics: An unsupervised learning approach in NAMD for deriving high probability transition pathways of biomolecular systems | John Vant Arizona State University |
| 15:55-16:15 | High throughput docking pipeline highlights differential response to isoprene | Martin Kulke Michigan State University |
| 16:15-16:45 | Discussion | |
| 18:00-20:00 | Group Dinner | |
Thursday, August 11: Day 2 Zoom webinar link
|
Time (CT)* |
Title |
Speaker |
| 08:30-09:00 | Breakfast |
|
| 09:00-09:20 | Bridging machine-learning-based dimensionality reduction and free-energy calculations |
Chris Chipot NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 09:20-09:40 | Absolute protein-ligand binding free-energy calculations using NAMD and BFEE2 |
Haohao Fu Nankai University |
| 09:40-10:00 | Coupling VMD to NAMD with the Colvars Dashboard, and a discussion of alchemical output formats |
Jérôme Hénin CNRS IBPC |
| 10:00-10:20 | Mass zero constrained dynamics for polarizable systems... and beyond |
Sara Bonella EPFL |
| 10:20-10:30 | Discussion | |
| 10:30-10:45 | Coffee Break | |
| 10:45-11:05 | Dispersion corrections to neural network potentials | Christopher Rowley Carleton University |
| 11:05-11:25 | Combining MD and ML to predict mechanical preoperties of proteins | Marcelo Melo Auburn University |
| 11:25-11:45 | QwikFold and why we still need Modeller | Diego Gomes Auburn University |
| 11:45-12:05 | Towards all-atoms sampling of membrane configurations using non-equilibrium molecular dynamics | Florence Szczepaniak Université de Lorraine |
| 12:05-12:25 | Discussion | |
| 12:25-13:10 | Lunch Break | |
| 13:10-13:30 | Accelerating NAMD with AMD GPUs | Julio Maia AMD |
| 13:30-13:50 | Latest CUDA developments for NAMD | David Clark NVIDIA |
| 13:50-14:10 | NAMD Xe enabling and optimization with SYCL | Ke Yue Intel |
| 14:10-15:00 | Discussion | |
| 15:00 | Workshop close | |