Computational Biophysics Workshop - Urbana, April 17-21, 2017
Program
(may be subject to small changes)Monday, April 17: Principles and Applications of Molecular Dynamics Simulations with NAMD
09:00-10:20 Introduction to Molecular Dynamics with NAMD, Emad Tajkhorshid10:20-10:40 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 Stone10:20-10:40 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 Methods10:20-10:40 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 Tajkhorshid10:20-10:40 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 Aksimentiev10:20-10:40 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