Advancing Molecular Simulation : From GPU Acceleration in Classical MD to Adaptive QM/MM Approaches

02:30 PM - 03:30 PM
Andreas Goetz, The University of California San Diego
National Center for Computational Sciences Seminar
Research Office Building (5700), Room MS-A106
Email: T. P. Straatsma

The recent years have witnessed exciting developments in the field of molecular simulation. Graphics processing units have expanded the simulation timescales that are accessible and brought supercomputer performance to the desktop. Meanwhile new methods such as adaptive quantum regions in multiscale QM/MM approaches are opening new application fields. This talk covers related developments in the Amber software package for biomolecular simulations. It first highlights the massive improvements in performance of classical molecular dynamics brought on by the GPU revolution, enabling routine simulations on the microsecond timescale. Important aspects of numerical precision, accuracy and validation of the implementation are also discussed. Next, the presentation covers new technologies for multiscale QM/MM simulations, including a new interface to external QM software packages for ab initio and DFT based simulations, as well as approaches for adaptively changing the QM region during a simulation. The methods are highlighted with application examples ranging from small molecule reactions in aqueous solution to absorption spectra in proteins.


Dr. Goetz is a candidate for a staff position within the Scientific Computing Group of the National Center for Computational Sciences.





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