Jay Ponder Associate Professor
Department of Chemistry
Washington University in St. Louis
St. Louis, MO

Monday, November 7, 2011
3:00 pm (CT)
3269 Beckman Institute

Abstract

The AMOEBA force field uses permanent atomic multipole moments through the quadrupole and classical induced atomic dipoles to model electrostatic interactions. It implements a modified Thole polarization damping scheme in an attempt to provide a force field applicable to multiple electrostatic environments and phases. At present the model is parameterized for water, ions, proteins, nucleic acids and a variety of small organics. Some of the key issues involved in design and development of AMOEBA will be discussed. This is followed by simulation results for a series of examples, including peptides, proteins, solvation free energy, and binding. Systemic differences between polarizable models and traditional mean-field force fields will be highlighted.