Computational Biophysics Workshop - Universidad Andres Bello, Chile, Jan. 26-29, 2015
Combining Cryo-Electron Microscopy & Biomolecular Simulations: Discoveries Through a Computer Microscope
Tutorials
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
- Molecular Dynamics Flexible Fitting (MDFF)
Describes how to flexibly fit atomic structures into density maps using the MDFF method. This method can be used to obtain atomic models of macromolecular complexes by combining X-ray structures and cry-electron microscopy maps.
- 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
