Statistical Mechanics, Statistical Error, Validation and Parameterization in Atomistic Simulations of Soft Materials

Monday, December 16, 2013 - 9:15am - 9:45am
Lind 305
Michael Shirts (University of Virginia)
When performing simulations of soft materials such as proteins and polymers, physical properties of interest always have associated statistical uncertainty. This inability to calculate properties exactly and understand the uncertainties precisely is one of the most important factors limiting our understanding how predictive such simulations actually are, as well as limiting the ability to improve the parameterization of force fields for these materials.

I will discuss several topics related to improving the reliability and consistency of such simulations, placing them in the context of community needs for molecular simulation to be truly useful, reliable and predictive in molecular design and research. For example, I will discuss uncertainty quantification and minimization as well as validation of thermodynamic ensembles. I will discuss our efforts to benchmark free energy calculation methods and systems, both for small molecules and for proteins-ligand binding energies, including error estimates and sensitivity to simulation parameters. Finally, I will discuss ongoing efforts to improve parameterization of biomolecular force fields using experimental data, including Bayesian approaches.
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