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Computational Biophysics Workshop - Dalian Institute of Chemical Physics, July 9-13, 2018

Below are planned tutorials listed by workshop day. More TCBG tutorials are available here.

Monday, July 9: Introduction to MD and VMD/NAMD

• Using VMD
• NAMD Tutorial

Tuesday, July 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
• Methods for Calculating Potentials of Mean Force

Wednesday, July 11: Protein-ligand Binding; Force-field Parametrization

• Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
• Parameterizing Small Molecules Using Force Field Toolkit (ffTK)

Thursday, July 12: Simulating Membrane Proteins; Fitting to Cryo-EM Maps

• Membrane Proteins Tutorial
• Molecular Dynamics Flexible Fitting (MDFF)

Friday, July 13: Complex Reaction Pathways & QM/MM Simulations

• NAMD-QM/MM Tutorial