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VijayPande wrote:In many ways, I think they are still several years behind us. If you take a look at the proteins they simulated, it's the systems we first folded several years ago (eg villin). The systems we're publishing now fold 1000x slower than villin and they would not be able to study the folding of those systems with their current approach. With that said, it's really neat to see what dedicated hardware can do and they've done very nice work.
PS I think it's wrong to say that this supercomputer has "set a protein folding record." I also don't think they claim that.
I wonder just how many Runs/Clones they ran to verify the statistical validity of the claim that this is always true, or just worked for the particular case(s) that they ran.The computer performed two types of simulations of well-studied systems: In the first, Anton's 100-microsecond simulations of the protein domain FiP35 show that the domain folds and unfolds in the same progression of steps each time—a surprise to some researchers.
See also http://folding.stanford.edu/English/Papers#ntoc4The second simulation involved a longer, one-millisecond study of the dynamics of the already folded protein bovine pancreatic trypsin inhibitor (BPTI), which explored the intricate motions of protein in water. Results were published in Science (2010, 330, 341).
Note that he carefully compares their system to other supercomputers, thereby excluding virtual supercomputers like FAH. That doesn't minimize what he has actually achieved but I still don't see that we have a scietific "record" for MD. Where did that work come from? Maybe I should remove it from the title.Anton was built solely for the purpose of molecular dynamics (MD) simulations of the behavior of large biological molecules. The machine, which was completed more than a year ago, stakes its claim to fame on its ability to perform lengthy simulations that aren't possible on current supercomputers. The new results mark the first significant test of Anton's prowess.
That's an extremely important statement. We have to keep reminding the FAH donors of what that means from the perspective of a Donor.MD simulations, which track the motions of every atom in a large molecule, are limited in their time scales by computer power and architecture. It can take months for a supercomputing system to simulate only tens of microseconds of a protein's dynamics. But many proteins fold on the millisecond time scale.
Again comparing to current supercomputers.Anton, its creators report, is capable of performing millisecond-long simulations of systems containing tens of thousands of atoms in 100 days—100 times faster than with current supercomputers.
So it's hard for him to generate good statistics ... one Run/Clone at at time. If a protein folds correctly 99% of the time, FAH has to analyze enough different possible folding sequences to have some of them show up in the 1% ways that it might actually mis-fold.Once a simulation starts, it can't be adjusted. "You cannot change conditions on the fly; it has to be hands off," Schulten says. Only about 10% of protein-folding problems can be done this way, he adds.
Collaborating with FAH might be a benefit to both projects. In fact, all 45 might do well to collaborate. Presumably some of that happens at the scientific conferences that they attend.Recently, Shaw Research donated another Anton machine to the Pittsburgh Supercomputing Center for research use by universities and other nonprofit institutions through the National Resource for Biomedical Supercomputing.
Schulten's group is one of 45 that were allotted time on the machine by the National Science Foundation. His group began simulations last week, and "it's working very well," he says.
bruce wrote:That doesn't minimize what he has actually achieved but I still don't see that we have a scietific "record" for MD. Where did that work come from? Maybe I should remove it from the title.
Jorge1950 wrote:The WU processing ultra-large to Anton; It is undervalued.
I loved processing units Advanced. I was a mathematician and I liked the theme of the new methods.
But my productivity dropped to 40%, 100% original.
Be subvaloran in the extreme points of Advanced units. Perhaps it is the right policy, I do not know these details.
I retired from the Advanced WU to the CPU; and I would advise to withdraw. I am studying the case of WU to GPU, Advanced.
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