NAMD Developer Workshop - Chicago, August 10 - 11, 2022

Program

Locations:
  • 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.
    • [フレーム]

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

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