S3: Biological Macromolecules
University of Maryland, Baltimore
Explicit treatment of electronic polarizability in empirical force fields offers the potential to significantly improve the accuracy of molecular simulations of macromolecules in condensed phases.
Towards achieving this we have developed a polarizable force field based on the classical Drude oscillator model.
An overview of the model and the parameter optimization approach will be presented.
Results will then be presented on MD simulations of macromolecules including carbohydrates, proteins, lipids and nucleic acids with emphasis on the ability of the model to more accurately reproduce quantum mechanical and experimental data.
Results include microsecond molecular dynamics (MD) simulations of multiple proteins in explicit solvent.
In addition, the polarizable model more accurately treats cooperative helix formation of the (AAQAA)3 peptide and yields improved agreement with experiment for base flipping in DNA.
Data obtained to date indicate that the inclusion of explicit electronic polarizability leads to significant differences in the physical forces affecting the structure and dynamics of macromolecules, which can be investigated in a computationally tractable fashion in the context of the Drude model.