The Oxford e-Research Many-Core Seminar Series Trinity 2012 -"Structural Bioinformatics & Computational Chemistry"
Matthieu Chavent, University of Oxford
- 25th April '12 from 01:00 pm to 02:00 pm
- Computer Science Lecture Theatre B
With advances in experimental structure determination, the size of biological assemblies keeps expanding. Studying such huge structures is part of the challenges faced by modern biology. Furthermore, very long molecular simulations of the order of milliseconds are required to accurately model some biological phenomena. To tackle these issues, massively parallel molecular simulations are used to understand the flexibility of huge macromolecular systems. Areas of theoretical chemistry and computational biology have already experienced significant progress with the advent of programmable graphics cards, which can drastically accelerate molecular simulations. These simulation approaches produce an incredible amount of data that must be visualized and analysed, however current molecular viewers cannot handle such large amounts of data. So it has now become important to reuse the GPUs for their genuine purpose: accelerating visualization.During this talk, I will present results of dynamic simulations, using NAMD program, obtained on a supercomputer with 196 GPUs. I will then present recent works on molecular visualization using the same GPU technology to accelerate rendering of huge molecular systems.