The electrical properties of proteins in solution are important for their structure and function. Computational biophysics studies of proteins need accurate parameters to ensure that numerical simulations match physical reality. Past work in this eld has compared the electrical properties of proteins obtained from dielectric spectroscopy to numerical simulations of proteins in water with adjustment of pKa values to try to capture the inevitable changes in electrical conformation that will occur in a complex structure such as a folded protein. However, fundamental veri cation of the charge parameters of the amino acid building blocks in common molecular dynamics software packages with electrical experiments needs to be performed to have increased con dence in the results from numerical simulations. The aim of this thesis is to start from a fundamental building block, the single amino acid alanine, and to compare numerical simulations of this amino acid in water using parameters from commonly used charge structures in CHARMM, GROMOS, and OPLS, with electrical parameters obtained from dielectric spectroscopy experiments in the GHz range. To this end, multiple molecular dynamics simulations were performed to accurately determine how these different charge structures yield different dielectric increments. Additionally, a commercial RF dielectric measurement probe was modi ed to perform measurements on solutions containing alanine at different concentrations. Using regression, the dielectric increment of alanine is readily determined and compared with the numerical simulations. The results indicate that the CHARMM and OPLS parameters seem to adequately capture the charge con guration of alanine in solution, while the GROMOS parameters produce a dielectric increment but do not seem to adequately capture the charge con guration of alanine in solution. These studies lay the foundation for future studies of additional amino acids in solution as well as a stepping stone for larger simulations of the electrical properties of fully solvated proteins in solution.
College and Department
Ira A. Fulton College of Engineering and Technology; Electrical and Computer Engineering
BYU ScholarsArchive Citation
Smith, Joshua Dee, "Verifying Molecular Dynamics Using Dielectric Spectroscopy" (2014). Theses and Dissertations. 4221.
alanine, amino acid, CHARMM, dielectric, dielectric increment, dielectric probe, dielectric response, dielectric spectroscopy, dipole, dipole moment, Dipole Moment Watcher, displacement current, GROMOS, l-alanine, Laplace, material properties, molecular dynamics, OPLS, partial charges, permittivity, permittivity spectra, relative permittivity, simulation, spectroscopy, system dipole moment, TIP3P, Visual Molecular Dynamics