Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018

Program

(subject to changes)

Location: Beckman Institute, Room 5602

Monday, September 10: Alchemical and Geometrical Free-Energy Calculations

09:00-09:20          Welcome and Brief Overview , Emad Tajkhorshid
09:20-09:45          Applications of Enhanced Sampling and Free-Energy Calculation Methods in Modern Biophysical Problems, Emad Tajkhorshid
09:45-10:00          Introduction to Alchemical and Geometrical Free-Energy Calculations, Chris Chipot
10:00-10:20          Coffee Break
10:20-12:20          Alchemical and Geometrical Free-Energy Calculations in NAMD, Chris Chipot
12:20-12:40          Q & A
12:40-14:00          Lunch Break
14:00-15:20          Tutorials
15:20-15:40          Coffee Break
15:40-18:00          Tutorials

Tuesday, September 11: Transition Path Sampling Methods and Constant pH Simulations

09:00-10:20          Transition Path Sampling Methods, Chris Chipot
10:20-10:40          Coffee Break
10:40-12:00          Hybrid Non-Equilibrium Molecular Dynamics/Metropolis Monte Carlo Calculations for Constant pH Simulations, Brian K. Radak
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, September 12: Geometrical Transformations and Collective Variables

09:00-10:20          Geometrical Free-Energy Methods: Strengths and Limitations, Jérôme Hénin
10:20-10:40          Coffee Break
10:40-11:40          Designing, Implementing and Optimizing Collective Variables in VMD and NAMD, Jérôme Hénin
11:40-12:00          Q & A
12:00-13:20          Lunch Break
13:20-15:30          Tutorials
15:30-16:30          Coffee Break + Meet 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)

Thursday, September 13: Specialized Algorithms for Enhanced Ergodic Sampling

09:00-10:20          Protein-Ligand Standard Binding Free-Energy Calculations, Chris Chipot
10:20-10:40          Coffee Break
10:40-12:00          Accelerating Convergence of Free-Energy Calculation with Replica Exchange Solute Tempering, Wei Jiang
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

Friday, September 14: Complex Reaction Pathways

09:00-10:20          Exploring Complex Reaction Pathways Part I, Mahmoud Moradi
10:20-10:40          Coffee Break
10:40-12:00          Exploring Complex Reaction Pathways Part II, Mahmoud Moradi
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