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Overview Week 1

Overview Week 1. Monday Intro & Logistics VMD & Assignments Wednesday Student VMD Presentations Friday Student VMD Presentations. Introductions. LaTech: Tom Bishop UNO: Steve Rick LSU: Michal Brylinski & Dorel Moldovan Xavier: Neil McIntyre. Students. LaTech: James Solow

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Overview Week 1

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  1. Overview Week 1 • Monday • Intro & Logistics • VMD & Assignments • Wednesday • Student VMD Presentations • Friday • Student VMD Presentations

  2. Introductions • LaTech: Tom Bishop • UNO: Steve Rick • LSU: Michal Brylinski & Dorel Moldovan • Xavier: Neil McIntyre

  3. Students • LaTech: • James Solow • Shawn Cole • UNO: • LSU: • Southern: • Xavier: Neil McIntyre

  4. Instructors Contact • Tom Bishop: • bishop@latech.edu • bishoptc@gmail.com • Steve Rick: • srick@uno.edu

  5. Students Contacts

  6. Student Survey • Major? • Grad/Ugrad? • Computer System Available? • Windows • Linux • PC

  7. LONI Accounts & Allocation • LONI login request https://allocations.loni.org/login_request.php and then request to be added to the allocation named "loni_lasigma_md" All the instructors are already added to this allocation.

  8. Syllabus • The syllabus is still evolving it's on google docs at • https://docs.google.com/document/d/1VbGo2VSuJIsNdN2mf2Er7YJnf4K_s9lkcPOgDrRSmSE/edit

  9. Description • Molecular Dynamics is an introduction to mastering the art of molecular modeling and dynamics simulations with an emphasis on high performance computing and modeling biomolecular systems. It will be team taught and meet once a week for video lectures. Each student will conduct a molecular simulation project. Students who take this course will learn how to configure a computer cluster (ideally a Little Fe but any two computers and a network switch can be used), install and utilize freely available molecular visualization, analysis and dynamics software tools, construct systems and run simulations on local and remote computing resources. Course work and lectures will essential structural biology and theoretical considerations from basic numerical integration techniques (e.g. Verlet algorithm, Ewald summations) to advanced thermodynamic considerations (e.g. replica exchange and free energy calculations). Projects are designed to explore an important biological application, proper use of an advanced simulation technique, performance characterization (e.g. numeric and performance analysis of gpu vs. traditional cpu))

  10. Objectives • Students who take this course will learn how to: • assemble and configure a computer cluster (LIttle Fe or similar) • perform molecular graphics and analysis of static structures • run molecular dynamics simulations using freely available software • run simulations on local and remote computing resources • analyze molecular dynamics trajectories • Do Computational Biology.

  11. Useful Books and Sites • This will be maintained as a separate document that I expect all to update. • Classic Texts: • M.P.Allen & D.J. Tildesley, Computer Simulations of Liquids, Oxford Science Publications • D.C. Rapaport, The Art of Molecular Dynamics Simultion, Cambridge University Press • J.M. Haile, Molecular Dynamics Simulation Elementary Methods, Wiley-Interscience Publication

  12. Online from NCBIwww.ncbi.nlm.nih.gov • Molecular Biology of the Cell. 4th edition. • Molecular Biology of the Cell. 4th edition. • Alberts B, Johnson A, Lewis J, et al. • New York: Garland Science; 2002.

  13. Modeling Sites/Software • NAMD/VMD: http://www.ks.uiuc.edu • AMBER: http://ambermd.org/ • Charmm • GROMACS • LAMMPS • Tinker • ESPResSo • “Molecular Modeling Software” on wikipedia

  14. Visualizations Software • RasMol: • Pymol: • VMD: • Jmol: java based, • Protein DataBank • MDL Chime

  15. Assignments & Projects • M: Weekly video lecture • W/F: Weekly student presentations/howtos • Each Student will give a final 1hr presentation on a project of their choosing

  16. VMD: Getting StartedVisual Molecular Dynamics www.ks.uiuc.edu follow “Software → VMD” • You may have to create an account to download it • Precompiled for any system architecture • Also installed on LONI systems • Need Xwindows to make work

  17. Downloading from PDB • In VMD you can directly down load a molecule from the Protein Databank • Www.rcsb.org

  18. Toms' Tips • Tom will show you how to download 1bpti • Make quick set of graphics • Make a quick set of presentations

  19. Assignment Number 1 • Download install VMD and namd on your system • What is the RCSB? • http://www.rcsb.org • Review Shape & Structure of Proteins in • Molecular Biology of the Cell at • http://www.ncbi.nlm.nih.gov/books/NBK26830/#A410

  20. Modeling VMD Assignment • Molecular Display of Single Peptide Bond • Backbone • Find molecules w/ following structural elements in the RCSB and tell their story using VMD • alpha-helix • Coiled-coil • beta-sheet both parallel and anti-parallel • A higher order fold (e.g. zinc finger)

  21. Wednesday and Friday Plans • Presentations from Students & Faculty

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