Posted on 01/01/2007 6:38:13 AM PST by texas booster
From a paper in the Journal of the American Chemical Society concerning nanotubes:
The folding of proteins in confined spaces is a ubiquitous theme in biological and biomaterial applications, including folding in chaperones and pores, nanotube-based drug delivery, and cotranslational folding of nascent peptides in the ribosomal exit tunnel. The role of confinement on peptide conformational equilibrium has thus gained much interest in recent years, and a natural first hypothesis to investigate is the role of confinement alone in protein conformational preferences.
...
Still, there exists a growing body of evidence to suggest that molecular water plays a role in the conformational preferences and assembly of biomolecular systems. For example, it has been suggested that the addition of crowding agents or chemical denaturants destabilizes proteins by affecting the structure of water. Moreover, the character of water in confined environments is expected to differ significantly from that in bulk.
...
What role does water play in the stability of confined proteins? To address this question, we have simulated a well-characterized 23-residue helical peptide inside six fully solvated single-walled CNTs with diameters ranging from 15 to 35 Å. For each tube modeled, 1000 independent molecular dynamics trajectories were started from the fully helical and extended states (Figures 1 and 2a). Simulations were performed on the Folding@Home distributed computing network as described previously using the AMBER- 99 helix-coil force field and the TIP3P water model in the NVT ensemble at the approximate midpoint temperature of 305 K (89F). With individual trajectories on the 100-300 ns time scale and an aggregate time exceeding 2.5 ms, our extensive sampling allows us to extract equilibrium thermodynamic data.
(Please click on the above link for the full paper on Nanotube Confinement Denatures Protein Helices)
Yes I can tell what happened.
Your box exploded.
Actually it looks like the Double Gromacs core that this work units uses encountered an out-of-range error and gave you an Early_Unit_End. I have had several of these, all on p33xx work units.
Looking at your points charts I see that you were credited for two work units today, one for 19 points and one for 40 points. That is a sure sign of a EUE caused by work unit errors.
The server seems to connect OK, and there do not seem to be any other issues with overclocking. It is possible that the SSE boost is the source of the problem but I haven't been able to confirm it.
Stanford will tighten up the boundaries of these work units within a week, once they discover the source of the EUEs.
http://folding.extremeoverclocking.com/user_summary.php?s=&u=168262
Link to your daily points, with a pretty graph.
It's given me another p3301, we'll see if I'm lucky enough not to be injured by more flying glass. Must be a problem with their p33xx's
My p2124 is on step 96 and should be through soon.
My SSE boost shows to be ok.
I like that. It is pretty. Bookmarked. Thanks.
Almost done building my new rig - AMD3800+X2 / ATI X1900
Should smoke those little proteins.
Will the MB have 2 CPUs? The new SMP betas are pumping out about 1,000 ppd for every system. Add in the GPU clients (not sure if they will work together), for 600 ppd, you could have a real barn burner.
The GPU can run as fast as possible, will use a moderate amount of CPU just for housekeeping, and the CPU probably can run a second core at about 25% - 40%.
Just be sure not to load Office, any games or other useful stuff. You are spending all this money for F@H. ;)
Congrats on your first completed work unit for F@H.
http://folding.extremeoverclocking.com/user_summary.php?s=&u=205119
Ping us if you have any questions!
TB
Thanks! I was going to write in and brag, but you beat me to it. I can't put much processor towards it, but every little bit helps. There'll be some more coming if I can get a certain notebook power connector fixed.
My UPS has saved my butt six times so far according to the software.
I got a new dual core CPU installed and running with a folding process assigned to each one.
Lets see what that does to your production. You have been hovering around 350 ppd since mid-December.
I have one dual core system and when it exclusively folds (almost never) it pops out the points.
I probably should consider UPS(s). My power goes out a few minutes at a time once a month or more. And roughly once or twice every 6 months, it will be out an hour or two.
Recently, I've had very few incidents of losing WU's, but yesterday the power was out for a few minutes and the backup file on one machine was corrupted. With my backup system I was able to restore the file in a few minutes. Probably saved about 40 hours of Folding.
BTW, thanks to FReepers for pointing me to the fact that you can run F@H as a service rather than having to rely on a screen saver or running app. Multiple people use this computer, so the service makes a world of difference for keeping it crunching.
Better yet, did anyone get a PS3? I don't want one for gaming (I have a Wii for that), but its folding potential is enormous.
Well I'm safely in the top 7500 of all folders and headed your way. Another few week and I'll overtake you (feels bad to overtake you, everyone else felt good).
Joseph
Thanks for that!
Yeah, I've been watching you steaming up my six. Congratulations on the top 7500! I'll feel honored to wave as you go by!
Just as an FYI:
The FAHMonitor will be offline for awhile tomorrow (Saturday) as I move my servers into a new rack.
You may see some red machines for a bit.
Honey.... I'm HOME !!!!!!!!
I know that you keep your ego in check, since network admins can be humbled very fast by a stupid vendor doing stupid things (Cisc*, Micros*ft, etc).
Somehow we all knew that you would be much happier producing 20,000 ppd rather than 2,000.
Very glad to have you back!
And to wardbob, who ever you be, thank you for joining our ragged little band!
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