Seminar room RB35 (Roslagstullsbacken 35, the SBC house)
Description
Molecular Dynamics (MD) simulations of large-scale biomolecular systems demand immense resources of computing power. As an alternative to the typical CPU clusters, the latest generations of Graphics Processing Units (GPUs) have emerged as a viable platform for acceleration of computationally intensive tasks. Optimal utilization of the power of the GPUs for molecular simulations though requires a remake of the classical simulation algorithms to fit in the new stream-computing paradigm, as presented by the GPU architecture.
In this talk I will introduce the streaming architecture of the GPUs; show examples of how existing MD algorithms have been adapted to optimally utilize it; and present the OpenMM library where the algorithms have been implemented. OpenMM is integrated in the next major Gromacs release and provides the core of the popular Folding@Home project.
