Gromacs

Support

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    Before seeking support for an issue to do with using GROMACS it is recommend that you first:

    • check the GROMACS Manual, which has a lot of detail and key information within,
    • consult the documentation for any relevant GROMACS tools by using gromacstool -h,
    • search or browse this website, in particular the FAQ list,
    • search the mailing lists,
    • search the internet using a search engine such as Google,
    • check the GROMACS Bugzilla as the error encountered may be a bug. (Before suggesting the existence of a bug on the mailing list, please ensure error is reproducible, and before submitting a request for Bugzilla, have set of files that developers can use to reproduce the error.) Some known bugs are documented here: Known Bugs.

    Do not email a developer or list subscriber personally unless your question pertains directly to their published work. If an email to a mailing list didn't get a reply, reconsider the points in the Mailing List Etiquette and try again.

    When posting a request for assistance be sure to

    • cite your GROMACS version number (and if it's not the most recent, try installing that first!),
    • describe your simulation system (e.g. protein name, protein size, solvent, ions, box type, box size, force field),
    • describe your simulation preparation before the problem arose,
    • copy and paste your input command lines,
    • consider including your .mdp file or the relevant portion of your .top or .log file,
    • consider uploading a relevant image or PDF to a file hosting service and providing the URL in your email so as to illustrate your observations,
    • inspect all your output files, stderr and stdout for information,
    • copy and paste any error message (look in both the .log file and stdout),
    • say why you thought the output was not what you expected,
    • use good netiquette, avoiding ALL CAPS, bad spelling and punctuation, txtspk, perso. abbrs, etc.,
    • include as much of the previous discussion in the thread as you can (nobody else can remember the context of the discussion quite as well as you can),
    • reply to an email list digest only after changing the subject to something descriptive,
    • reply to an email list digest only after removing the content not relevant to your post, and
    • try to sound like you've worked on solving your own problem, and are not just stealing other people's time (we'll know if you haven't done such work!).

    Nobody will be much interested in assertions that have been filtered through your head. This is because computers are literal, and if you really understood how to manage things correctly, you wouldn't be having a problem. Hence, people who might help want to see copy-pasted real input and output, not what you think they were or should have been!

    If you wish to suggest the existence of a bug in GROMACS, and haven't provided the above information, then the bug is in the way you present your information.

    Page last modified 10:51, 23 Mar 2012 by mabraham