Molecular Dynamics Investigation of Alanine: Enthalpic Control of Dihedral Free Energy
DOI:
https://doi.org/10.54097/qqcvtv18Keywords:
Molecular dynamics (MD), Alanine dihedral analysis, Free energy landscapes, Enthalpy vs. entropy CP2K force field, AmberTools SimulationsAbstract
This project investigates the molecular dynamics of the amino acid alanine and examines the relationship between Gibbs free energy, dihedral angles, and bond lengths. The primary objective is to determine whether entropy or enthalpy plays a more significant role in governing the free energy landscape. Our findings indicate that the magnitude of free energy exhibits minimal variation with temperature, suggesting that the torsional barrier is predominantly enthalpic in origin.
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[1] Allen, M. P., & Tildesley, D. J. (2017). Computer Simulation of Liquids (2nd ed.). Oxford University Press. https://doi. org/ 10.1093/oso/9780198803195.001.0001.
[2] Frenkel, D., & Smit, B. (2001). Understanding Molecular Simulation: From Algorithms to Applications (2nd ed.). Academic Press.
[3] Verlet, L. (1967). Computer “experiments” on classical fluids. I. Thermodynamical properties of Lennard-Jones molecules. Physical Review, 159(1), 98–103. https://doi.org/ 10.1103/ PhysRev. 159.98.
[4] Hutter, J., Iannuzzi, M., Schiffmann, F., & VandeVondele, J. (2014). CP2K: An electronic structure and molecular dynamics software package - Quickstep: Efficient and accurate electronic structure calculations. Wiley Interdisciplinary Reviews: Computational Molecular Science, 4(1), 15–25. https://doi. org/ 10. 1002/wcms.1159.
[5] Case, D. A., Ben-Shalom, I. Y., Brozell, S. R., Cerutti, D. S., Cheatham, T. E., & Kollman, P. A. (2020). Amber 2020. University of California, San Francisco.
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