BAGIM is an active community of Boston area scientists bringing together people from diverse fields of modeling and informatics to impact life and health sciences. BAGIM strives to create a forum for great scientific discussions covering a wide range of topics including data management, visualization, computational chemistry, drug discovery, protein structure, molecular modeling, structure-based drug design, data mining, software tools, and the sharing of goals and experiences. Our community is made up of participants from academia, government, and industry whose goal is to engage in the discussion of science involving a synthesis of theory and technology. Discussions sponsored by BAGIM are targeted to the needs and interests of informatics scientists, computational chemists, medicinal chemists, and statisticians. BAGIM also provides opportunities for networking within these disciplines as well as an arena for the dissemination of information of specific interest to the membership.

Friday, April 7, 2017

BAGIM Event: Dr. Todd Martinez, Wednesday May 3rd at Vertex Pharmaceuticals, starting at 5:30pm

Dr. Todd J. Martinez, of Stanford University, will present "Quantum Chemistry and Ab Initio Molecular Dynamics on Graphical Processing Units" on Wednesday, May 3rd, 2017, at Vertex Pharmaceuticals.  Dr. Martinez will present at 7pm, but networking and refreshments will precede the talk starting at 5:30pm.

Please RSVP with your full name to help us plan for the event and to help speed security check in.

Abstract: Solution of the electronic structure problem (often known as “quantum chemistry”) is a critical step in much of chemical simulation. For example, quantum chemistry is required to fit parameters for empirical force fields and also for ab initio molecular dynamics approaches which eschew force fields altogether. The recent introduction of stream processors such as graphical processing units (GPUs) promises to accelerate quantum chemistry calculations. We provide an overview of the differences between GPUs and conventional CPUs and discuss how quantum chemistry algorithms can be redesigned to use GPUs effectively. We show that accelerations of up to three orders of magnitude can be achieved (relative to conventional CPU implementations) by exploiting GPUs with redesigned algorithms. Several applications enabled by these advances are discussed, including an assessment of the size of QM regions needed to achieve convergence in QM/MM methods. Finally, we discuss the ab initio nanoreactor, which uses GPU-enabled ab initio molecular dynamics to discover reaction networks. We present the overall concept of the nanoreactor and some first applications to complex reaction networks in combustion and prebiotic chemistry.

BAGIM is sponsored by Dassault Systemes, DNASTAR, LabAnswer, OpenEye Scientific, Schrodinger, Silicon Therapeutics, Acellera, Acpharis, Cambridge Crystallographic Data Centre, Chemical Computing Group, Dotmatics, Cresset, Cyrus Biotechnology, Optibrium, Team Arrayo, and Scilligence