Computational Biophysics Workshop - Urbana, April 17-21, 2017

Program

(may be subject to small changes)

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Monday, April 17: Principles and Applications of Molecular Dynamics Simulations with NAMD

09:00-10:20          Introduction to Molecular Dynamics with NAMD, Emad Tajkhorshid
10:20-10:40          Coffee Break
10:40-11:40          Applications of Molecular Dynamics with NAMD, Emad Tajkhorshid
11:40-12:00          Introduction to Molecular Dynamics Flexible Fitting, Ryan McGreevy
12:00-12:20          Q & A
12:20-14:00          Lunch Break
14:00-15:20          Tutorials
15:20-15:40          Coffee Break
15:40-18:00          Tutorials

Tuesday, April 18: Molecular Simulation, Analysis, and Visualization with QwikMD and VMD on the Amazon Cloud

09:00-10:20          Visualizing Biomolecules in VMD, John Stone
10:20-10:40          Coffee Break
10:40-12:00          Introduction to QwikMD and Amazon Cloud, João Ribeiro
12:00-12:20          Q & A
12:20-14:00          Lunch Break
14:00-15:20          Tutorials
15:20-15:40          Coffee Break
15:40-18:00          Tutorials

Wednesday, April 19: Methods for Computing Free-Energies in Biomolecular Systems (Chris Chipot)

09:00-10:20          A General Overview of Free-Energy Methods
10:20-10:40          Coffee Break
10:40-12:00          Accurate Calculation of Protein-Ligand Binding Energies
12:00-12:20          Q & A
12:20-14:00          Lunch Break
14:00-15:20          Tutorials
15:20-15:40          Coffee Break
15:40-18:00          Tutorials

Thursday, April 20: Parameterization for Classical Force Fields with FFTK

09:00-10:20          Introduction to Classical Force Fields - Topology, Parameters, and Structure Files, Emad Tajkhorshid
10:20-10:40          Coffee Break
10:40-11:40          Introduction to Force Field Toolkit, Christopher Mayne
11:40-12:00          Q & A
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-16:30          Coffee Break + Q & A with the Developers
16:30-16:50          Group Picture and Social
16:50-18:00          Tutorials
19:00-21:00          Workshop Dinner (place to be determined; sign in during the workshop)

Friday, April 21: Computational Research at the Interface of Physics, Biology, and Nanotechnology

09:00-10:20          Introduction to modeling and simulation of DNA systems, Alek Aksimentiev
10:20-10:40          Coffee Break
10:40-12:00          Introduction to simulations of bacterial cells, Zan Luthey-Schulten
12:00-12:20          Q & A
12:20-14:00          Lunch Break
14:00-15:20          Tutorials
15:20-15:40          Coffee Break
15:40-18:00          Tutorials