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the Walker Molecular Dynamics lab



Video extract from the NVIDIA GTC 2010 Conference in San Jose, CA. The Walker Molecular Dynamics Lab's work on accelerating the AMBER Molecular Dynamics package with GPUs is featured in the keynote speech by the CEO of NVIDIA. (Click here to download the video if the above player does not work)


What we do...

The research focus of the Walker Molecular Dynamics (, based at the San Diego Supercomputer Center at the University of California San Diego, encompasses the fields of computational chemistry, molecular biology and high performance computing. The lab is particularly interested in the development of efficient algorithms parallel and GPU accelerated computation of Quantum Mechanical and hybrid Quantum/Molecular Mechanical (QM/MM) techniques as well as improvements in the computational efficiency and accuracy of classical MM dynamics simulations. The research also focuses on the use of MM and QM/MM Molecular Dynamics algorithms for the determination of physical and chemical properties of protein based systems.

The lab is funded through a combination of grants from the National Science Foundation (NSF), National Insitutes of Health (NIH), the University of California, NVIDIA, Microsoft, Intel and the UK Foreign and Commonwealth Office, Department for Business, Innovation and Skills. Practical applications of the techniques developed in the lab include the development of next generation viral inhibitors, improvements in bio-ethanol production, drug discovery and advanced algorithms for high performance of scientific application on supercomputers.

The lab is also closely involved with the development of the AMBER molecular dynamics software and leads the GPU acceleration efforts which have resulted in AMBER's pmemd.cuda molecular dynamics engine being the world's fastest molecular dynamics package on commodity hardware.