Computational Biophysics Workshop - July 17 - 21, 2023
Program
Monday, July 17:
| 09:00 | Application of molecular dynamics to biomolecular modeling MD-Introduction.pdf, Overcoming_Timescale.pdf |
Emad Tajkhorshid NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | Ab initio protein structure modeling with Alphafold in VMD | Diego E.B. Gomes Department of Physics, Auburn University |
| 11:45 | Quick setup and analysis of NAMD simulations with QwikMD | Rafael Bernardi Department of Physics, Auburn University |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: VMD and NAMD tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: QwikMD tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
Tuesday, July 18:
| 09:00 | Enhanced sampling and free energy calculations in NAMD - Part I EnhancedSamplingRecording.mp4 |
Mahmoud Moradi Department of Chemistry and Biochemistry University of Arkansas |
| 10:30 | Coffee Break | |
| 10:45 | Enhanced sampling and free energy calculations in NAMD - Part II EnhancedSamplingRecording2.mp4 |
Mahmoud Moradi Department of Chemistry and Biochemistry University of Arkansas |
| 11:30 | Free energy calculations at QM/MM level | Rafael Bernardi Department of Physics, Auburn University |
| 12:10 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Free energy and enhanced sampling tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Free energy and enhanced sampling tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
Wednesday, July 19:
| 09:00 | VMD+ Special features and capabilities VMD+recording.mp4 |
John Stone NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 10:00 | Advanced visualization, figures and movies in VMD AdvancedVisVMDrecording.mp4, AdvancedVisVMD.pdf |
Mariano Spivak NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | NAMD 3.0 features, performance and capabilites NAMD3recording.mp4, NAMD3.pdf |
David Hardy NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 11:45 | Force field parameterization with FFTK FFTKrecording.mp4, FFTK.pdf |
Mariano Spivak NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: FFTK tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: PMF tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes |
Thursday, July 20:
| 09:00 | Molecular simulation at the interface of biology and nanotechnology Bionanotechnology.mp4 |
Aleksei Aksimentiev NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 10:30 | Coffee Break | |
| 10:45 | Multi-resolution simulations with ARBD ARBD.mp4 |
Christopher Maffeo NIH Resource for Macromolecular Modeling and Visualization University of Illinois at Urbana-Champaign |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Modeling nanopores for sequencing DNA | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes, C. Maffeo |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Other tutorial | H.S. Hasdemir, Y. Li, P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes, C. Maffeo |
Friday, July 21:
| 09:00 | Molecular Dynamics in the Era of Exascale Computing | Rafael Bernardi Department of Physics, Auburn University |
| 09:30 | Advanced Analysis Methods: Network Analysis | Marcelo C.R. Melo Department of Physics, Auburn University |
| 10:30 | Coffee Break | |
| 10:45 | Introducing Cybershuttle: A platform to launch and control simulation jobs in HPC | Sudhakar Pamidighantam Cyberinfrastructure Integration Research Center, Indiana University |
| 11:45 | Cybershuttle for Molecular Dynamics Applications | Marcus Christie Cyberinfrastructure Integration Research Center, Indiana University |
| 12:15 | Q & A | |
| 12:30 | Lunch Break | |
| 14:00 | Hands-on tutorial session I: Cybershuttle tutorial | P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes, M. Christie |
| 15:30 | Coffee Break | |
| 15:45 | Hands-on tutorial session II: Other tutorial | P.S.F.C. Gomes, M.C.R. Melo, D.E.B. Gomes, M. Christie |