FR Folding@Home Project Update - Folding of Proteins in Nanotube Confinement

Journal of the American Chemical Society ^ | 02/07/2006 | Stanford University

[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)

[LonePalm]

My ATI card will probably arrive on Wednesday. Our company follows DoD holidays and closings.

Garde la Foi, mes amis! Nous nous sommes les sauveurs de la République! Maintenant et Toujours!
(Keep the Faith, my friends! We are the saviors of the Republic! Now and Forever!)
LonePalm, le Républicain du verre cassé (The Broken Glass Republican)

[texas booster]

Thank you for joining us and publicising the team. Have you been folding very long?

For any of the new folders please pop a note here if you have any problems.

TB

[brityank]

Thanks; my checkpoint is set for 15Min, but it only seems to do them at each step anyway:

[12:36:37] + Working...
[13:34:40] Writing local files
[13:34:40] Completed 12200000 out of 20000000 steps (61)
[15:45:36] Writing local files
[15:45:36] Completed 12400000 out of 20000000 steps (62)
[18:01:26] Writing local files
[18:01:26] Completed 12600000 out of 20000000 steps (63)
[18:36:34] + Working...


Not a problem; I learned on my company's laptop not to allow the IT mavens to upload/reboot my machine after they clobbered five hours I had devoted into a spreadsheet.

Oh, yes. They did hear me now! ;^)

[ken in texas]

Thanks for the new thread.

My compute resources have subsided a bit since first starting, but I now have another machine that should be able to fold for 3-4 months.

[paulat]

Bump!

C'mon, you guys...join the team!!

I can't believe I don't see more familiar names on our list!!

[JosephW]

Things are moving along swimmingly and I should be among the top 7500 folders in another day. However, with the new year, Egon's tool is giving me some really funny results. Looks like most of my WU won't finish until sometime 2 or 3 years out (I know it's an error, but it is funny).

At this rate I'm not sure how much of a help I'm going to be until about 2010 :)

[processing please hold]

I can't believe I don't see more familiar names on our list!!

I've thought the same thing. Oh well...

[dfwddr]

At this rate I'm not sure how much of a help I'm going to be until about 2010 :)

The best solution for you would be to shut down, oh for somewhere around 4-6 weeks. Your climbing into the top 10 way too fast, and I think this would be the best thing for you. Trust me ;)

[JosephW]

Relax, it's at least 5 weeks until I catch up to you, probab ly more like 7.

Since I don't have any upgrades on the horizon, you can expect me to average about 800ppd

[texas booster]

I have noticed the same accounting on the logs, where it only makes an entry after a step. When I looked closer I found additional entries on a system where F@H is shut down regularly.

---

[18:43:19] Assembly optimizations on if available.
[18:43:19] Entering M.D.
[18:43:39] (Starting from checkpoint)
[18:43:39] Protein: p2126_villin_sigd3
[18:43:39]
[18:43:39] Writing local files
[18:43:39] Using table 3
[18:43:40] Completed 3188807 out of 50000000 steps (6)
[18:43:40] Extra SSE boost OK.
[19:48:45] Writing local files
[19:48:45] Completed 3500000 out of 50000000 steps (7)
[21:33:01] Writing local files
[21:33:01] Completed 4000000 out of 50000000 steps (8)

Folding@Home Client Shutdown.

---

At least on this system, Win XP SP2, F@H GUI 5.03 does record shut downs between steps.

You should have made the IT mavens (coven?) recover the file. Nowadays spreadsheets keep writing open files to a temp file, that if all goes well, can usually be recovered by a competent IT dude / dudette.

[texas booster]

Looking at your points chart, it seems that you have lost a system, or had one stop reporting into Stanford.

http://folding.extremeoverclocking.com/user_summary.php?s=&u=197716

Once the ATI card is in, install the recommended drivers as listed here:

http://www.stanford.edu/group/pandegroup/folding/FAQ-ATI.html

Once installed, test F@H by looking at the logs. A sure sign of driver mismatch is completing a WU every minute - they are actually abnormal ends (abends) and do not contribute to actual research. One fella on another team recorded 202 points on 1,448 work units.

You should be able to complete a WU every day, boosting your ppd to 600 - 700 on just that machine. Add in a couple of other systems and you could easily be a 1,000 ppd producer.

Plus you can play any game made at full resolution.

[LonePalm]

Well, those charts are certainly better than my little, manually updated, POS spreadsheet.

Garde la Foi, mes amis! Nous nous sommes les sauveurs de la République! Maintenant et Toujours!
(Keep the Faith, my friends! We are the saviors of the Republic! Now and Forever!)
LonePalm, le Républicain du verre cassé (The Broken Glass Republican)

[Egon]

However, with the new year, Egon's tool is giving me some really funny results. Looks like most of my WU won't finish until sometime 2 or 3 years out (I know it's an error, but it is funny).

Yeah, that's a new feature I've added: REALLY long-term predictions.

F@H doesn't report years with their dates in the status file. Apparently, I failed to take that into consideration. Working on a fix now.

[Egon]

My shameless self-promotion for this thread:

If you're interested in tracking your folding machine(s) over the web, please Freepmail me.

Available features include:

• Timely snapshot of each machine's progress on it's current project
• Point values for project
• Estimated completion dates/times
• Warning indicators for machines that appear to have stopped communicating or folding
• Warnings for machines that won't make their deadline
• Team ranking status box (courtesy of EOC)
• Machine stats like PPD (points per day)
• Project comparison stats: PPD, average time taken to completion, etc.
• It's free-- and always will be
• ...other features as time permits, and people request

[Egon]

OK. Problem fixed, I think.

I'm going back through and looking for weird history entries turned in over the last day, and I'll attempt to correct them as well.

If, over the next couple of days, you notice any weird history entries, let me know the machine, date, and project, and I'll correct them.

Thanks!

[brityank]

Yes; that's a normal shutdown:

Folding@home Client Shutdown.


--- Opening Log file [December 6 04:57:54]


# Windows Graphical Edition ####################

Here's what a failed one gives:

[12:43:27] Writing local files
[12:43:27] Completed 495000 out of 750000 steps (66)


--- Opening Log file [December 6 00:36:00]


# Windows Graphical Edition ################

There's no shutdown, and the files are corrupted so it restarts from 0. I also find that the SSE Boost is missing, but a clean restart gets it back.

[texas booster]

I looked at this issue many months ago and needed a refresh. The info on recovering defective work units can be found here:

http://fahwiki.net/index.php/Howto_use_qd_to_debug_the_FAH_client

It may be wiki but it seems clean.

Sometime work units will calculate into improbable folding situations and will be killed off. Sometimes, what you seem to experience happens. I'll bet that your client databases are scrambled and need repair.

The qd utility refrenced above in wiki will sometimes fix queue.dat and allow you to recover your points.

Disclaimer: I have never taken the time to learn this utility and will not be able to for a week or so. However, if my 9:00 pm contribution is any indication (2 work units for 11 points) then I may need to learn it well.

[HangThemHigh]

My power company sees fit to provide power here at the house most of the time. A year or so ago, if I lost power or even a brief flicker, I had about a 30% chance of losing the WU in progress. The checkpoint file seemed to be getting corrupted in a power loss. It got bad enough that I wrote a script to back up the whole directory about once an hour to preclude massive losses.

Lately Stanford seems to have fixed the console version so that on lost power the previously saved checkpoint isn't corrupted. I'm assuming they have "fixed" this as I haven't had to restore the F@H directory from my backups in 6 mo. or so.

Perhaps the GUI version hasn't gotten the fix, or Windows ME (I run XP) prevents the fix from working somehow. Even before the fix, if I shut down the computer normally (vs. a power failure or hitting the reset button) the checkpoint file would survive.

Not sure this helps, just an observation.

[Egon]

Perhaps the GUI version hasn't gotten the fix, or Windows ME (I run XP) prevents the fix from working somehow.

I think it might be Windows ME, actually. I've had (until recently) a WinME machine folding with the console version. Every once in awhile, it would lock up, and upon restarting, the WU would invariably restart from scratch.

I haven't had this problem on any other OS.

[processing please hold]

[07:57:41] Project: 3301 (Run 3898, Clone 0, Gen 1)
[07:57:41]
[07:57:41] Assembly optimizations on if available.
[07:57:41] Entering M.D.
[07:57:48] Protein: p3301_ribcomp
[07:57:48]
[07:57:48] Writing local files
[07:57:49] Extra SSE2 boost OK.
[07:57:50] Writing local files
[07:57:50] Completed 0 out of 25000 steps (0)
[08:04:26] Writing local files

[12:35:30] Writing local files
[12:35:31] Completed 21500 out of 25000 steps (86)
[12:37:56] Quit 101 - Fatal error: Box exploding.
[12:37:56]
[12:37:56] Simulation instability has been encountered. The run has entered a
[12:37:56] state from which no further progress can be made.
[12:37:56] This may be the correct result of the simulation, however if you
[12:37:56] often see other project units terminating early like this
[12:37:56] too, you may wish to check the stability of your computer (issues
[12:37:56] such as high temperature, overclocking, etc.).
[12:37:56] Going to send back what have done.
[12:37:56] logfile size: 8556
[12:37:56] - Writing 9109 bytes of core data to disk...
[12:37:56] ... Done.
[12:37:56]
[12:37:56] Folding@home Core Shutdown: EARLY_UNIT_END
[12:38:00] CoreStatus = 72 (114)
[12:38:00] Sending work to server

[12:38:00] + Attempting to send results
[12:38:03] + Results successfully sent
[12:38:03] Thank you for your contribution to Folding@Home.
[12:38:07] - Preparing to get new work unit...
[12:38:07] + Attempting to get work packet
[12:38:07] - Connecting to assignment server
[12:38:08] - Successful: assigned to (171.64.65.83).
[12:38:08] + News From Folding@Home: Welcome to Folding@Home
[12:38:08] Loaded queue successfully.
[12:45:39] + Closed connections
[12:45:44] [12:45:44] + Processing work unit
[12:45:44] Core required: FahCore_79.exe
[12:45:44] Core found.
[12:45:44] Working on Unit 07 [January 3 12:45:44]
[12:45:44] + Working ...
[12:45:44]
[12:45:44] *------------------------------*
[12:45:44] Folding@Home Double Gromacs Core
[12:45:44] Version 1.91 (April 11, 2006)
[12:45:44]
[12:45:44] Preparing to commence simulation
[12:45:44] - Looking at optimizations...
[12:45:44] - Created dyn
[12:45:44] - Files status OK
[12:45:45] - Expanded 1381063 -> 5334069 (decompressed 386.2 percent)
[12:45:45] - Starting from initial work packet
[12:45:45]
[12:45:45] Project: 3301 (Run 3645, Clone 0, Gen 1)
[12:45:45]
[12:45:46] Assembly optimizations on if available.
[12:45:46] Entering M.D.
[12:45:52] Protein: p3301_ribcomp
[12:45:52]
[12:45:52] Writing local files
[12:45:53] Extra SSE2 boost OK.
[12:45:55] Writing local files
[12:45:55] Completed 0 out of 25000 steps (0)
[14:00:41] Writing local files
[14:00:41] Completed 6000 out of 25000 steps (24)
[14:08:30] Quit 101 - Fatal error: Box exploding.
[14:08:30]
[14:08:30] Simulation instability has been encountered. The run has entered a
[14:08:30] state from which no further progress can be made.
[14:08:30] This may be the correct result of the simulation, however if you
[14:08:30] often see other project units terminating early like this
[14:08:30] too, you may wish to check the stability of your computer (issues
[14:08:30] such as high temperature, overclocking, etc.).
[14:08:30] Going to send back what have done.
[14:08:30] logfile size: 8454
[14:08:30] - Writing 9007 bytes of core data to disk...
[14:08:30] ... Done.
[14:08:31]
[14:08:31] Folding@home Core Shutdown: EARLY_UNIT_END
[14:08:33] CoreStatus = 72 (114)
[14:08:33] Sending work to server

Ok, there was one more that did the same thing, I didn't post it because too much space. I deleted the steps between the first and last numbered steps to save space. By looking at it can you tell what happened?