Computational Biophysics

1. Using VMD 2.VMD Images and Movies Tutorial 3. Aquaporins with the VMD MultiSeq Tool 4. Visualization and Analysis of CPMD data with VMD 5. NAMD Tutorial 6. NAMD Paper 7. Membrane Proteins Tutorial 8. A Tutorial to Set Up Alchemical Free Energy Perturbation Calculations in NAMD 9. A Tutorial to Set Up Adaptive Biasing Force Calculations 10. Building Gramicidin A 11. Parameterizing a Novel Residue 12. Evolution of Translation: Class-I aminoacyl-tRNA synthetases 13. Evolution of Translation: EF-Tu 14. Evolution of Translation: Ribosome 15. Sequence Alignment Algorithms 16. Topology File Tutorial 17. User-Defined Forces in NAMD 18. Bionanotechnology Tutorial 19. Shape-Based Coarse Graining 20. Stretching Deca-Alanine 21. Simulation of Water Permeation through Nanotubes 22. Steered Molecular Dynamics Tutorials