Posts by Jeremy

1) Message boards : Number crunching : Energy reference point (Message 53898)
Posted 21 Jun 2008 by Jeremy
Post:
In the rosetta beta graphics the energy is positive or negative. Is the 0 energy point the energy of the starting molecule?

(Perhaps this should be at the science board, my apologies.)
2) Message boards : Rosetta@home Science : What is a "Decoy"? (Message 53895)
Posted 21 Jun 2008 by Jeremy
Post:
I'm not an expert but here is what I think. A starting structure is the state of the molecule before you start optimizing, a decoy is the result of the optimization (lowest energy structure).

If there was no limit on run time there would be virtually endless decoys. And one of them would be the actual folding of the molecule.

There is virtually no maximum of decoys.

Many computers generate decoys, they are sent in and the best one is picked. It would take years(or more) to do that with one normal computer.

I hope this anwsers your question and that I didn't make any horrible mistakes.
3) Message boards : Number crunching : Shorter WU time (Message 53842)
Posted 19 Jun 2008 by Jeremy
Post:
Oh thanks for your answers,

I'm back at rosetta now, but I did put my WU time on 1hour. The advantage is that I can see many different projects.

However I don't want to miss out on the complex molecules.
4) Message boards : Number crunching : Shorter WU time (Message 53768)
Posted 18 Jun 2008 by Jeremy
Post:
Does rosetta give other tasks (other apps or other molecules) if you change your prefrence time to 1hour for example.

What are the (pro's and) conta's for taking short WU times?
5) Message boards : Number crunching : to many validate/compute errors (Message 53761)
Posted 18 Jun 2008 by Jeremy
Post:
100% agreed
6) Message boards : Number crunching : teraFLOPS estimate? (Message 53760)
Posted 18 Jun 2008 by Jeremy
Post:
Due to all the errors I did move away to Poem@home parialy, i keep checking if there are Beta WU's. The main thing keeping me at rosetta are the Graphics of the beta version. I'm sure this doesn't count for everyone but the errors are a pain.

7) Message boards : Number crunching : Minirosetta v1.28 bug thread (Message 53699)
Posted 15 Jun 2008 by Jeremy
Post:
I had the same problem, it was taking about 2 hours to go from 96% to 97% done. Can't seem to find it in my results page.
8) Message boards : Number crunching : Minirosetta v1.28 bug thread (Message 53684)
Posted 14 Jun 2008 by Jeremy
Post:
(Almoust) all my Rosettamini tasks are failing again, just like with the previous versions.

resultid=171215792
resultid=171206890
resultid=171001609
resultid=170828593
resultid=170797357

I'm switching to ralf not so i can get some Rosettabeta tasks.
9) Message boards : Number crunching : What happened to minirosetta? (Message 53556)
Posted 5 Jun 2008 by Jeremy
Post:
I have Rosetta Beta 5.96 tasks exclusively atm, can't say that that is a bad thing. I like the graphics.
10) Message boards : Number crunching : CASP8 (Message 53441)
Posted 29 May 2008 by Jeremy
Post:
I tought CASP was a blind prediction test, why do I see native structures in my WU 's? wuid=152643758 for example


This is just a guess, but it's possible that not all WUs that have CASP8 in the name are actually CASP8 targets; some might be new optimizations that the team are doing for CASP8 and first testing on proteins with known shapes before moving them over to the real deal.

Can anyone confirm this?
11) Message boards : Number crunching : CASP8 (Message 53423)
Posted 28 May 2008 by Jeremy
Post:
I tought CASP was a blind prediction test, why do I see native structures in my WU 's? wuid=152643758 for example
12) Message boards : Number crunching : minirosetta v1.24 bug thread (Message 53302)
Posted 23 May 2008 by Jeremy
Post:
Same issue as before: Compute errors, almoust every minirosetta task, the normal rosetta tasks work perfectly.
See my tasks for details
13) Message boards : Number crunching : minirosetta v1.19 bug thread (Message 53248)
Posted 21 May 2008 by Jeremy
Post:
I have had nothing but Compute errors with the mini version of rosetta. See this page
http://boinc.bakerlab.org/rosetta/results.php?userid=259031

I'd rather only have the normal ones for 2 reasons. One it keeps giving errors so the cpu time isn't putt to use. It doesn't have propper grafics, but I've read that that is not a priority.

I'd like to help debugging this application by sending whatever information you need.

Here is my host sheet.
http://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=812509






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