Computational Biophysics Workshop - October 18 - 22, 2021

Program

  • All sessions broadcasted through Zoom. You can access recordings on our YouTube channel

    • 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