Properties from Molecular Dynamics
6. Properties from Molecular Dynamics#
In this last set of exercises, you will be introduced to practical applications of molecular dynamics. After a brief treatment of advanced simulation concepts and an introduction to protein biochemistry, you will analyse the folding of the Trp-cage miniprotein.
🎯 Learning goals
Learn how to simulate solvated systems
Run a production grade simulation using a GPU
Simulate protein folding of a small peptide
Perform a basic analysis of an MD trajectory
📖 Chapter in script
Chapter 6 - Advanced Molecular Dynamics Techniques
📚 Resources
Simmerling, C., Strockbine, B., and Roitberg, A.E., All-Atom Structure Prediction and Folding Simulations of a Stable Protein J. Am. Chem. Soc. 2002, 124, 38, 11258–11259 https://doi.org/10.1021/ja0273851
Braun, E., Gilmer, J., Mayes, H. B., Mobley, D. L. ., Monroe, J. I., Prasad, S., & Zuckerman, D. M. . (2018). Best Practices for Foundations in Molecular Simulations [Article v1.0]. Living Journal of Computational Molecular Science, 1(1), 5957. https://doi.org/10.33011/livecoms.1.1.5957