New open-source software permits faster desktop computer simulations of molecular motion

A snapshot from a molecular dynamic simulation of the folding of a mutant protein found in chicken intestines. New open-source software permits faster simulations of molecular motion on desktop computers.

Whether vibrating in place or taking part in protein folding to ensure cells function properly, molecules are never still. Simulating molecular motions provides researchers with information critical to designing vaccines and helps them decipher the bases of certain diseases, such as Alzheimer's and Parkinson's, that result from molecular motion gone awry. In the past, researchers needed either supercomputers or large computer clusters to run simulations. Or they had to be content to run only a tiny fraction of the process on their desktop computers.

But a new open-source software package developed at Stanford University is making it possible to do complex simulations of molecular motion on desktop computers at much faster speeds than has been previously possible.

"Simulations that used to take three years can now be completed in a few days," said Vijay Pande, an associate professor of chemistry at Stanford University and principal investigator of the Open Molecular Mechanics (OpenMM) project. "With this first release of OpenMM, we focused on small molecular systems simulated and saw speedups of 100 times faster than before."

OpenMM is a collaborative project between Pande's lab and Simbios, the National Center for Physics-based Simulation of Biological Structures at Stanford, which is supported by the National Institutes of Health. The project is described in a paper that was scheduled to be posted online Feb. 3 in the "Early View" section of the Journal of Computational Chemistry.

The key to the accelerated simulations OpenMM makes possible is the advantage it takes of current graphics processors (GPUs), which cost just a few hundred dollars. At its core, OpenMM makes use of GPU acceleration, a set of advanced hardware and software technologies that enable GPUs, working in concert with the system's central processor (CPU), to accelerate applications beyond just creating or manipulating graphics.

The icing on the molecular-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 open, cross platform tools that allow researchers to focus on solving problems with their GPU of choice."

NVIDIA is similarly committed to OpenMM. "OpenMM promises to further increase the adoption of GPU technology among the molecular dynamics community," said Andy Keane, general manager, GPU Computing at NVIDIA. "We'll continue our close collaboration with Stanford on OpenMM so that current and future libraries can maximally leverage the power of the GPU."

OpenMM incorporates specially developed algorithms that allow MD software to take full advantage of the GPU architecture. In fact, the OpenMM code is at the heart of the GPU implementations of the Folding@home project, which uses the horsepower of GPUs and CPUs in computers around the world to simulate protein folding. The current release uses an implicit solvent model, in which all the surrounding fluid, such as water, is represented as one continuous medium, rather than having each water molecule represented individually (an explicit solvent model). Future releases will allow the modeling of explicit solvent. ###

A free workshop on OpenMM and OpenMM Zephyr (http://simtk.org/home/zephyr), an easy-to-use application for running and visualizing accelerated MD simulations, will be offered sometime in the next three months. Anyone interested in learning about using OpenMM and OpenMM Zephyr will be welcome. A workshop on Feb. 12 is already filled. For more information on the workshop, or a symposium on molecular dynamics held the day after each workshop, email simbiosfeedback@stanford.edu.

Contact: Louis Bergeron louisb3@stanford.edu 650-725-1944 Stanford University

President Obama Weekly Address 02/21/09 PODCAST VIDEO TEXT

SATURDAY, February 21, 2009 WEEKLY ADDRESS BY THE PRESIDENT TO THE NATION PODCAST OF THIS ARTICLE Download MP3 4.4 mb

THE PRESIDENT: Earlier this week, I signed into law the American Recovery and Reinvestment Act -- the most sweeping economic recovery plan in history. Because of this plan, 3.5 million Americans will now go to work doing the work that America needs done.

I'm grateful to Congress, governors and mayors across the country, and to all of you whose support made this critical step possible.

Because of what we did together, there will now be shovels in the ground, cranes in the air, and workers rebuilding our crumbling roads and bridges, and repairing our faulty levees and dams.

Because of what we did, companies -- large and small -- that produce renewable energy can now apply for loan guarantees and tax credits and find ways to grow, instead of laying people off; and families can lower their energy bills by weatherizing their homes.

Because of what we did, our children can now graduate from 21st century schools and millions more can do what was unaffordable just last week -- and get their college degree.

Because of what we did, lives will be saved and health care costs will be cut with new computerized medical records.

Because of what we did, there will now be police on the beat, firefighters on the job, and teachers preparing lesson plans who thought they would not be able to continue pursuing their critical missions. And ensure that all of this is done with an unprecedented level of transparency and accountability, I have assigned a team of managers to make sure that precious tax dollars are invested wisely and well.

Because of what we did, 95 percent of all working families will get a tax cut -- in keeping with a promise I made on the campaign. And I'm pleased to announce that this morning, the Treasury Department began directing employers to reduce the amount of taxes withheld from paychecks -- meaning that by April 1st, a typical family will begin taking home at least $65 more every month. Never before in our history has a tax cut taken effect faster or gone to so many hardworking Americans.

But as important as it was that I was able to sign this plan into law, it is only a first step on the road to economic recovery. And we can't fail to complete the journey. That will require stemming the spread of foreclosures and falling home values, and doing all we can to help responsible homeowners stay in their homes, which is exactly what the housing plan I announced last week will help us do.

It will require stabilizing and repairing our banking system, and getting credit flowing again to families and businesses. It will require reforming the broken regulatory system that made this crisis possible, and recognizing that it's only by setting and enforcing 21st century rules of the road that we can build a thriving economy.

And it will require doing all we can to get exploding deficits under control as our economy begins to recover. That work begins on Monday, when I will convene a fiscal summit of independent experts and unions, advocacy groups and members of Congress, to discuss how we can cut the trillion-dollar deficit that we've inherited. On Tuesday, I will speak to the nation about our urgent national priorities. And on Thursday, I'll release a budget that's sober in its assessments, honest in its accounting, and lays out in detail my strategy for investing in what we need, cutting what we don't, and restoring fiscal discipline.

No single piece of this broad economic recovery can, by itself, meet the demands that have been placed on us. We can't help people find work or pay their bills unless we unlock credit for families and businesses. We can't solve our housing crisis unless we help people find work so that they can make payments on their homes. We can't produce shared prosperity without firm rules of the road, and we can't generate sustained growth without getting our deficits under control. In short, we cannot successfully address any of our problems without addressing them all. And that is exactly what the strategy we are pursuing is designed to do.

None of this will be easy. The road ahead will be long and full of hazards. But I am confident that we, as a people, have the strength and wisdom to carry out this strategy and overcome this crisis. And if we do, our economy -- and our country -- will be better and stronger for it.

Thank you.