Computational Biophysics Workshop - October 18 - 22, 2021
Program
Monday, October 18:
|
Time (CT)* |
Title |
Speaker |
| 09:00 | Application of molecular dynamics to biomolecular modeling Recording (YouTube) |
Emad Tajkhorshid NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | Quick setup and analysis of NAMD simulations with QwikMD Recording (YouTube) |
Rafael Bernardi Department of Physics, Auburn University |
| 11:45 | Ab initio protein structure modeling with Alphafold in VMD Recording (YouTube) |
Rafael Bernardi Department of Physics, Auburn University |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: QwikMD tutorial Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: VMD and NAMD tutorial |
Tuesday, October 19:
|
Time (CT)* |
Title |
Speaker |
| 09:00 | Enhanced sampling and free energy calculations in NAMD - Part I Recording (YouTube) |
Chris Chipot NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | Enhanced sampling and free energy calculations in NAMD - Part II Recording (YouTube) |
Chris Chipot NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 11:30 | Collective variables Recording (YouTube) |
Jérôme Hénin CNRS, Laboratoire de Biochimie Théorique Institut de Biologie Physico-Chimique, Paris, France |
| 12:10 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Free energy and enhanced sampling tutorial Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Free energy and enhanced sampling tutorial Recording (YouTube) |
Archit Vasan NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
Wednesday, October 20:
|
Time (CT)* |
Title |
Speaker |
| 09:00 | VMD+ Special features and capabilities Recording (YouTube) |
John Stone NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:00 | Advanced visualization, figures and movies in VMD Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | NAMD+ Special features, performance and capabilites Recording (YouTube) |
David Hardy NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 11:45 | Force field parameterization with FFTK Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Creating images and movies with VMD and FFTK tutorial Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Other tutorial |
Thursday, October 21:
|
Time (CT)* |
Title |
Speaker |
| 09:00 | Whole cell simulation with Lattice Microbes - Part I Recording (YouTube) |
Zan Luthey-Schulten NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | Whole cell simulation with Lattice Microbes - Part II Recording (YouTube) |
Zan Luthey-Schulten NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 12:10 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Lattice Microbes tutorial Recording (YouTube) |
Troy Brier NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Lattice Microbes tutorial |
Friday, October 22:
|
Time (CT)* |
Title |
Speaker |
| 09:00 | Nanotechnology with molecular simulation Recording (YouTube) |
Aleksei Aksimentiev NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:00 | Using NAMD and VMD in the Cloud Recording (YouTube) |
Barry Isralewitz NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | QM/MM calculations with NAMD Recording (YouTube) |
Rafael Bernardi Department of Physics, Auburn University |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Membrane proteins tutorial Recording (YouTube) |
Mariano Spivak NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Other tutorial Recording (YouTube) |
Christopher Maffeo NIH Resource for Macromolecular Modeling and Bioinformatics University of Illinois at Urbana-Champaign |