Computational Biophysics Workshop - Tokyo, Japan, March 5, 2018
Tutorials
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Below is a list of the tutorials used at the summer school.
Please
click here to see a page with the updated versions of these tutorials.
- Using VMD
An introduction to VMD and its capabilities
- NAMD Tutorial
An introduction to NAMD and its capabilities
- A Tutorial on Alchemical Free Energy Perturbation
Calculations in NAMD
Discusses setting up the system and calculations needed for free energy calculations of alchemical transformations within NAMD
- Protein:ligand Standard Binding Free Energies: A Tutorial for Alchemical and Geometrical Transformations
Demonstrates that the standard binding free energy of a protein:ligand complex can be determined accurately by means of restrained computer simulations. In the tutorial, calculation of the contribution due to restraints follows two distinct routes, an alchemical one and a geometrical one. The methodology is illustrated by the association of a small, proline-rich peptide to a tyrosine kinase.