From analyzing the results of the searches all of you have done over the past week we have made a real breakthrough! The puzzle that emerged at the end of last week was that, while very low rms structures were generated in your searches, they typically had much higher energies than the native structure. It was as if you were playing golf, and the hole you were trying to land in was surrounded by an elevated barrier. I was puzzling over this while bicycling up the hill behind my house Sunday morning, and had an idea which I incorporated into the program and tested later in the day. The really neat result is that when I took the lowest rmsd structures that you found, and started calculations from them, the energy dropped dramatically, and the rmsd decreased significantly as well, as if the barrier had been replaced by a gentle slope down into the hole. Since Sunday, Vatson, a graduate student, Bin, a postdoctoral researcher in my group, and I have found that this dramatic movement towards the native structure occurs for a number of different protein systems.

David Kim is now preparing the latest version of the code for distribution on BOINC, and you will hopefully receive work units with the improved algorithm sometime tomorrow. If he has time, David will include the graphics option Jack Schonbrun has developed which shows quite vividly what is going on during the calculations. We think it is going to be a hit!

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Wow... this is very nice to hear. I honestly can't wait to start getting some of those units now. ;o)

I know I've said this too many times already but THANK YOU for keeping everyone up to date! It makes this project extremely enjoyable.

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Jeff's Computer Farm

Sounds promising

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wondering why we bother anymore

Excellent news. Also great that we get this information shared with us so quickly too. Makes running the project much more worthwhile!

Bok

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Free-DC

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That's great news - did you get inspiration from the hill you were cycling on?

And thanks for sharing - it's one of the things that makes this project special.

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*** Join BOINC@Australia today ***

We are of course all elated to hear of the quick success. David's message also tells us on what incredibly short timescales this project operates. Another reason to return our WUs as quickly as possible to give the Baker team a chance to quickly react to the feedback which they get from our crunched WUs. So if at all possible, don't keep more WUs in your local cache than absolutely necessary. I believe the success of this project is driven by the brain power of the Baker lab scientists even more so than by the donated rosetta@home CPU cycles (they are of course also important, so keep on crunching). Just my two cents on the recent discussion on 'hoarding' WUs. -Hermann

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That's great news - did you get inspiration from the hill you were cycling on?

And thanks for sharing - it's one of the things that makes this project special.

For some it is falling apples, for others it is cycling over hills ...

Local minimas ...

But, I do agree ... even having one message each day in one thread makes a significant difference.

Not to find fault, or to point a finger. BUT, the contrast where a project scientist posts regularly makes a huge impact. In SETI@Home, Rom and Matt post occassionally but, Dr. Anderson? Never. Is that a mistake? Possibly. I know why he does not (and there is more than one reason), but it CAN look like avoiding your participants.

This is the "cost" of the "free" computing resources. :)

Hmmm, just another side idea ... LHC@Home has a "known issues" page ... we MAY want to consider starting one here too ... of course, it needs to be updated ... :)

Even, and especially if there is no resolution ... "nope, have not found it yet ... but we are still looking and we made this change ..." kind of thing ...

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Thanks for the update David, can't wait to run the tweaked code.

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From analyzing the results of the searches all of you have done over the past week we have made a real breakthrough! We think it is going to be a hit!

Your enthusiasm is contagious! Thank you very much for sharing it! :)

I know I feel with Rosetta@home much closer to the excitement of scientific discovery. I can share with you the fun of what it means to be a scientist and what motivates you!

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Regards,
Bob P.

David........

Just an invitation to you to pop over to our lil dc forum and post a lil something (should you wish)about this project.

A message from you would increase this projects profile at our board and perhaps encourage more of our membership to give it a try.

I hope to see you stop by.

You can find our forum via the bottom link in my sig.

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wondering why we bother anymore

Thanks for the update David, this sounds very exciting.

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Team CFVault.com
http://www.cfvault.com

Ahhh!

This is what I love about science! I'm so excited to be a small part of this project.

I think it's time to up my resource share over here. So many exciting things going on!

Kathryn

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Kathryn :o)
The BOINC FAQ Service
The Unofficial BOINC Wiki
The Trac System
More BOINC information than you can shake a stick of RAM at.

...David Kim is now preparing the latest version of the code for distribution on BOINC, and you will hopefully receive work units with the improved algorithm sometime tomorrow....

I'm as enthused as everyone else in this thread. But someone always has to spoil the moment...that's me. I must admit that because of the instability of the project over the past week or so I reduced my resource share to Rosetta from 45% to 16%. I will be happy to reverse it when I observe stability again. My results page indicates that I have several WUs that are either in progress or past due. As far as I know I processed and returned everything that was sent to me. Lost credit & lost science? This is a psychological downer.

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Fantastic!....thanks for the timely update once again, David. It certainly will keep the interest in the project front and centre.....Cheers, Rog.

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My results page indicates that I have several WUs that are either in progress or past due. As far as I know I processed and returned everything that was sent to me. Lost credit & lost science? This is a psychological downer.

Your latest results look fine, which is a wonderful thing and an upper not a downer. Perhaps the stability issue has been solved? If it was me I would up my resource share to experimentally find out if it has been solved. Just a suggestion.

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Regards,
Bob P.

My results page indicates that I have several WUs that are either in progress or past due. As far as I know I processed and returned everything that was sent to me. Lost credit & lost science? This is a psychological downer.

Your latest results look fine, which is a wonderful thing and an upper not a downer. Perhaps the stability issue has been solved? If it was me I would up my resource share to experimentally find out if it has been solved. Just a suggestion.

Just yesterday (Nov 8) in another forum GoTo David Kim said "Once we have our architecture set and STABLE we will set up a regular maintenance schedule for backups, purging, cleanup, etc. Our goal is to have a system that may be capable of handling Seti-like usage."

I construe that things -- by their own admission -- are not stable yet.

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The servers are running normal and are stable, however, we will be upgrading the servers and adding more hardware to distribute the work in the future. So with respect to the new architecture, once we have it setup we will start a regular maintenance schedule.

I would continue to run the project "Nothing But Idle Time". The results reporting inconsistency you were seeing was most likely due to the recent down times. The boinc manager should handle the project work distribution should any project be down so I don't think you need to worry about changing the resource share as another project will be picked up if one is down.

I must admit that because of the instability of the project over the past week or so I reduced my resource share to Rosetta from 45% to 16%. I will be happy to reverse it when I observe stability again. My results page indicates that I have several WUs that are either in progress or past due. As far as I know I processed and returned everything that was sent to me. Lost credit & lost science? This is a psychological downer.

Some of the older versions of the BOINC Client Software could "lose" work because of errors during the transfer process. The later versions have additional checks to help prevent this problem.

Without knowing which version you are running it is hard to say why the work may have been "lost".

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Congratulations, David!

Yes, those "Aha!" experiences soemtimes come at weird times!

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[b]"I'm trying to maintain a shred of dignity in this world." - Me[/b]