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New open-source software permits faster desktop computer simulations of molecular motion
Date:2/5/2009

olecular-simulation cake is that the software has no allegiance to any particular brand of GPU, meaning it is, as computer geeks like to say, "brand agnostic." OpenMM will enable molecular dynamics (MD) simulations to work on most of the high-end GPUs used today in laptop and desktop computers.

This is a boon to MD developers. Converting their code to run on just one GPU product is a challenging project by itself. And until now, if developers wanted to accelerate their MD software on different brands of GPUs, they would have to write multiple versions of their code. OpenMM provides a common interface.

"OpenMM will allow researchers to focus on the science at hand instead of the hardware," Pande said. "Researchers will see a jump in productivity and resourcefulness from computers they already own." With OpenMM, researchers can use GPUs to perform massively parallel calculations.

OpenMM fits squarely with Simbios' mission of providing computational tools to stimulate research in biology and medicine, according to Russ Altman, principal investigator of Simbios and chair of the Department of Bioengineering at Stanford. "OpenMM will be a tool that unifies the MD community," he said. "Instead of difficult, disparate efforts to recode existing MD packages to enjoy the speedups provided by GPUs, OpenMM will bring GPUs to existing packages and allow researchers to focus on discovery."

The new release of OpenMM includes a version of the widely used MD package GROMACS that integrates the OpenMM library, enabling it to be sped up on high-end NVIDIA and AMD/ATI graphics cards. Close collaborations with AMD (which owns the ATI brand) and NVIDIA were critical for getting OpenMM to run on their GPUs.

"Cross-platform solutions like OpenMM enable a much broader community of researchers to leverage GPU acceleration capabilities like ATI Stream technology" said Patricia Harrell, director of Stream Computing, AMD. "AMD is committed to supporting o
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Contact: Louis Bergeron
louisb3@stanford.edu
650-725-1944
Stanford University
Source:Eurekalert

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