Computational Biophysics Workshop - Urbana, October 17-21, 2016

Program

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

Beckman Institute, Tower Room 2269

09:00-10:20          Introduction to Molecular Dynamics with NAMD, Emad Tajkhorshid
10:20-10:40          Coffee Break
10:40-12:00          Using NAMD: Examples from Modern Research, Emad Tajkhorshid
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-15:50          Coffee Break
15:50-18:00          Tutorials

Tuesday, October 18: Molecular Simulation, Analysis, and Visualization with QwikMD and VMD

Beckman Institute, Tower Room 3269

09:00-10:20          Introduction to QwikMD, Rafael Bernardi and Joao Ribeiro
10:20-10:40          Coffee Break
10:40-12:00          Visualizing Biomolecules with VMD, Jodi Hadden
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-15:50          Coffee Break
15:50-18:00          Tutorials

Wednesday, October 19: Parameterization for Classical Force Fields with FFTK

Beckman Institute, Tower Room 3269

09:00-10:20          Introduction to Classical Force Fields - Topology, Parameters, and Structure Files, Emad Tajkhorshid
10:20-10:40          Coffee Break
10:40-12:00          Introduction to Force Field Toolkit, Christopher Mayne
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-15:50          Coffee Break
15:50-15:30          Tutorials
16:30-18:00          Group Picture and Social

Thursday, October 20: Computational Research at the Interface of Physics, Biology, and Nanotechnology

Beckman Institute, Tower Room 3269

09:00-10:20          Introduction to Modeling and Simulations of Nucleic Acid Systems, Alek Aksimentiev
10:20-10:40          Coffee Break
10:40-12:00          Modeling the Interface Between Biological and Synthetic Materials, Alek Aksimentiev
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-15:50          Coffee Break
15:50-18:00          Tutorials

Lecture files

Friday, October 21: Principles and Applications of Molecular Dynamics Flexible Fitting

Beckman Institute, Tower Room 4269

09:00-10:20          Introduction to MDFF, Ryan McGreevy
10:20-10:40          Coffee Break
10:40-12:00          Using MDFF: Examples from Modern Research, Till Rudack
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-15:50          Coffee Break
15:50-18:00          Open Discussion in TCBG Innovation Courtyard