Post date: Aug 23, 2017 10:14:24 PM

The Computers in Chemistry Division of the American Chemical Society awarded Prof. Emilio Gallicchio of Brooklyn College the NVIDIA GPU Best Poster Award at the 254th ACS National Meeting & Exposition in Washington DC. Prof. Gallicchio's poster is entitled "Efficient GPU/OpenMM implementation of the AGBNP solvation model for macromolecular binding"


Emilio Gallicchio, egallicchio@brooklyn.cuny.edu, Denise Kilburg, Baofeng Zhang

Brooklyn College, Brooklyn, NY, and Doctoral Programs in Chemistry and Biochemistry, Graduate Center of the City University of New York, New York, NY

The poster describes the GPU implementation of the Analytic Generalized Born plus Non-Polar implicit solvent model (AGBNP) for the OpenMM molecular simulation package. As part of this work, novel recursive computational geometry algorithms have been developed to estimate volumes and surface areas of macromolecules. The Generalized Born pairwise descreening algorithm has been formulated to take advantage of the GPU architecture. The GPU implementation is 50 to 100 times faster than our best CPU implementation. Illustrative applications to binding free energy calculations are presented. OpenMM plugin: github.com/egallicc/openmm_gaussvol_plugin

The generous donation of an impressive Titan Xp GPU by NVIDIA is greatly appreciated. We will put it to good use!