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Thread: We're trying to minimize WHAT????

  1. #1
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    Question We're trying to minimize WHAT????

    I thought we would be trying to minimize crease energy. But looking at the charts for the top ten results it is clear that the client is making no effort at all to minimize crease energy. None of the other charts look like there's any attempt to optimize them, either. So what is the client trying to minimize?


  2. #2
    The client itself minizes the energy. In the stats is shown the energy, because it tells us the real worth of the structure ....
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  3. #3
    Ol' retired IT geezer
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    Energy Graphs Trending UP

    dfGUI always reported that the RMS trended DOWN initially at least for the previous three proteins, BUT this is not the case with this client. It is reporting the "Energy" value, and in the three cases I've looked at so far, the trend is moving UP!!!

    I'm not sure if the RMS value that isn't shown until it gets to the server is trending down or not...

    Seems like the wrong direction though...

    My two cents worth...

    Ned

  4. #4
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    That's one of the things (energy going up - and down) I mentioned in http://www.free-dc.org/forum/showthr...&threadid=4567 - Howard replied saying that

    It may do great, it may not, but the important difference now is we are not using ANY information about the true structure now, it is true 'ab initio' prediction. We are treading on unexplored territory now. Thus even if the energy goes down, the RMSD may not, and vice-versa. We will watch how this run goes carefully, and 'tweak' parameters as we feel necessary for the next protein to try to improve things even more.
    Does seem a bit odd when compared to the good ol' RMS going down that we are used to

  5. #5
    More precisely, if you are looking at the graphs, the client is minimizing the 'fitness score'. This is a combination of crease energy, Secondary structure content compared to predicted, and Rgyr.
    Howard Feldman

  6. #6
    Ol' retired IT geezer
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    Apples and Oranges

    The client is minimizing the 'fitness score'. This is a combination of crease energy, Secondary structure content compared to predicted, and Rgyr.
    Ok, more calculations than previous client to do the comparisons... Hence, warmer CPU's.

    I can see that you expected the crease energy to be minimized with the fitness score and that's why you had the progress.txt report "energy"... However, if this is your new criteria, please use the "fitness score" in progress.txt so that we can easily see the success of the algorithm...

    My two cents worth...

    Ned

  7. #7
    progress.txt is NOT for human eyes...
    Howard Feldman

  8. #8
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    Originally posted by Brian the Fist
    progress.txt is NOT for human eyes...
    so why does the readme1st.txt file say

    To check progress while in quiet mode/running as a service, a file called
    "progress.txt" will be written to the directory where the program is installed
    so you can monitor its progress still

  9. #9
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    .. those of us running DF as a service aren't considered human? That really explains a lot. *snicker*
    www.thegenomecollective.com
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  10. #10
    I think what he meant was the last line in progress.txt isn't really intended for human eyes. The other information is quite readable by humans.

  11. #11
    Originally posted by tpdooley
    .. those of us running DF as a service aren't considered human? That really explains a lot. *snicker*
    Probably as good a reason as any why there are now only 1,505 active "participants" out of 26,458 registered...

  12. #12
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    Originally posted by Digital Parasite
    I think what he meant was the last line in progress.txt isn't really intended for human eyes. The other information is quite readable by humans.
    If that's the case then why is it there? What else is using (DF-wise, not 3rd party-wise) progress.txt for that info (iirc, the energy is also in filelist.txt)?


  13. #13
    It is there essentially for dfGUI. If you want to look at it, go ahead but don't interpret the contents too literally
    Howard Feldman

  14. #14
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    Originally posted by Brian the Fist
    It is there essentially for dfGUI. If you want to look at it, go ahead but don't interpret the contents too literally
    I won't - as long as you don't mind me using the value in my monitoring app

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