Computational Biophysics Workshop - Urbana, Illinois, September 10-14, 2018
Tutorials
Below are planned tutorials listed by workshop day. More TCBG tutorials are available here.
Monday, September 10: Alchemical and Geometrical Free-Energy Calculations
- A Tutorial on Alchemical Free Energy Perturbation Calculations in NAMD
- A Tutorial on Adaptive Biasing Force Calculations in NAMD
- Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
Tuesday, September 11: Transition Path Sampling Methods and Constant pH Simulations
- String Method with Swarms of Trajectories: A Tutorial for Free-energy Calculations along a Minimum-action Path
- Constant pH tutorial
Wednesday, September 12: Geometrical Transformations and Collective Variables
- Colvars module (source code and supporting material)
- Performing Metadynamics Simulations Using NAMD
- Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
- A Tutorial on Adaptive Biasing Force Calculations in NAMD
Thursday, September 13: Specialized Algorithms for Enhanced Ergodic Sampling
- Methods for calculating Potentials of Mean Force
- A Tutorial on One-dimensional Replica-exchange Umbrella Sampling
- Adaptive Multilevel Splitting Method: Isomerization of Alanine Dipeptide
