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    Simon Bray
    @simonbray:matrix.org
    [m]
    for me that works at least
    doesn't help with the workflow extraction issue though :/
    thepineapplepirate
    @thepineapplepirate
    drag and drop into the tool's input list?
    Simon Bray
    @simonbray:matrix.org
    [m]
    drag from the history to the tool input
    thepineapplepirate
    @thepineapplepirate
    that doesn't work on my end, wonder if its my browser. im using safari
    Simon Bray
    @simonbray:matrix.org
    [m]
    hm, interesting, could be
    I am not sure about your underlying issue
    thepineapplepirate
    @thepineapplepirate
    no problem man, i appreciate the support man! :)
    bgruening
    @bgruening:matrix.org
    [m]
    safari is known to cause problems
    I would not use it
    thepineapplepirate
    @thepineapplepirate
    so seems like i can drag and drop on chrome
    but i get this error when i run it
    "The server could not complete this request. Please verify your parameter settings, retry submission and contact the Galaxy Team if this error persists. A transcript of the submitted data is shown below."
    were u able to run it after dragging and dropping?
    Simon Bray
    @simonbray:matrix.org
    [m]
    I just tried now, no, I can't
    interesting that prmtop doesn't appear in the upload menu as a datatype option
    I wonder if that's related
    thepineapplepirate
    @thepineapplepirate
    yeah, i was just about to say that. so if u go and try to change the datatype, and search prmtop or inpcrd, they actually doesn't show up as an option
    Simon Bray
    @simonbray:matrix.org
    [m]
    but in your PR you have set display_in_upload="true" 😕
    how did you manage to set the datatype then?
    thepineapplepirate
    @thepineapplepirate
    its part of the tleap tool
    Simon Bray
    @simonbray:matrix.org
    [m]
    Ah
    thepineapplepirate
    @thepineapplepirate
    it outputs it as format 'prmtop' or 'inpcrd'
    you can rerun that history and see what it does
    if u rerun step 16
    Simon Bray
    @simonbray:matrix.org
    [m]
    I wonder if the extensions are really not enabled somehow on EU, if nothing is working
    thepineapplepirate
    @thepineapplepirate
    i think that's the issue, despite the merge it's not on there somehow
    it seems it was merged into the right repo, _release_21.09_europe
    Simon Bray
    @simonbray:matrix.org
    [m]
    ok, our sysadmin Gianmauro is looking at it, apparently they are indeed missing
    thepineapplepirate
    @thepineapplepirate
    ok, phew! at least we know what's going on. thanks Simon
    Simon Bray
    @simonbray:matrix.org
    [m]
    @thepineapplepirate in future, we need to edit https://github.com/usegalaxy-eu/infrastructure-playbook/blob/master/files/galaxy/config/datatypes_conf.xml for the changes to be shown on EU
    I haven't touched that file for a couple of years, I forgot that it existed 😅
    thepineapplepirate
    @thepineapplepirate
    haha, ok i see
    so in the case of new datatypes
    Simon Bray
    @simonbray:matrix.org
    [m]
    yep
    thepineapplepirate
    @thepineapplepirate
    we edit the actual data datatypes_conf.xml file
    as well as this
    is that why prmtop and inpcrd weren't showing up?
    Simon Bray
    @simonbray:matrix.org
    [m]
    yes
    the one in the Galaxy repo is the default configuration, but we are overriding it on EU with our own config file
    hence why both need to be updated
    thepineapplepirate
    @thepineapplepirate
    ok, that's good to know.
    thepineapplepirate
    @thepineapplepirate
    its working on the EU server now, so we good :)
    Simon Bray
    @simonbray:matrix.org
    [m]
    cool 👍️
    thepineapplepirate
    @thepineapplepirate
    @bhagirathbhatta838 On second thought, Langevin dynamics ('integrator = sd' in your mdp file) should be ok in this scenario. But in general it's worth keeping tabs on the integrators you use. Langevin dynamics is stochastic, which adds a degree of randomness into the system, and thus creates a simulation that is not entirely deterministic. This is done to help ensure constant temperature. In a real finite system, the atomic and molecular collisions would eventually lead to heat losses/gains that would influence a fluctuation in temperature. Langevin dynamics creates a 'dampening effect' at every time step, that helps reduce this loss, thus helping maintain constant temperature. you can think of this as greasing bearings in a wheel, a lubrication so to speak. regular md is ok, but for big systems that you are trying to simulate for longer periods of time, Langevin dynamics might be a good option.
    bgruening
    @bgruening:matrix.org
    [m]
    that might be interesting for us :)
    Simon Bray
    @simonbray:matrix.org
    [m]
    Lorraine used that for her master's thesis
    quite a nice library
    not sure if it makes sense to be wrapped in Galaxy though