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Thread: new protein though mor AA residues runs faster?

  1. #1

    new protein though mor AA residues runs faster?

    Is this due to the individuall residues being more 'difficult' to coform within a three d grid.. electropositivity et al...
    It's also been noted that the default upload speed has gone down to 2000 structures??
    Unless you're running Jeff Gilchrists well honed GuI with default value of 5000?
    Where's Howard?
    KWSN and 3DHQ..:|punch|:

  2. #2
    Howard was talking about bringing the new back end online soon so it is possible he set the default lower to 2000 because it is now online and can handle the load?

    And yes it seems this new larger protein folds much faster than the previous smaller one. Each protein is different, even two proteins with the same number of AA will fold at different speeds depending on their structure.

    As for dfGUI, if the default is now 2000 unless you are forcing it to use 5000 with the upload frequency box, it will also do 2000 and you will have to set your "# of Structures" box to 2000. Remember that offline clients always use 5000 structures for their buffer size.


  3. #3
    Bottom of the Top Ten TheOtherZaphod's Avatar
    Join Date
    May 2002
    zone 5 west
    I don't know the cause but you are definitely right aabout this one being both bigger, and faster.

    As far as the upload frequency goes I have taken manual control of mine with the -s switch, and uploadfreq= parm. I have a couple of machines that are always getting innterrupted; I put those two down to 1000 so that I don't lose as much work. I had all the other boxes at 10000 for a while last week, but I pushed them down to 3000 for the switchover. I may leave them there, or raise them to say 5000 for this week.
    Don't Panic

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