Problem with NAMD?

  1. Download and test NAMD 2.9, the most recent version.

  2. Direct questions regarding the tutorials to the Tutorial-L mailing list; check the archive first.

  3. Please check NamdWiki (particularly NamdTroubleshooting and NamdKnownBugs ), NAMD-L archive, release notes, user's guide, tutorials, and the rest of the NAMD web site resources.

    Search all NAMD resources:

  4. Please read How To Ask Questions The Smart Way, but do not pester Eric S. Raymond and Rick Moen (the authors of that page) with questions about NAMD or anything else.

  5. For problems compiling or running NAMD please review the release notes and Charm++ Installation and Usage Manual, check the NamdOn... pages at NamdWiki, and later summarize the resolution of your problem there that others may benefit from your experience. If you do not understand the errors generated by your compiler, queueing system, ssh, or mpiexec you should seek assistance from a local expert familiar with your setup.

  6. For questions about using NAMD please subscribe to NAMD-L and post your question there so that others may benefit from the discussion. Please avoid sending attachments to NAMD-L by posting any related files on your web site or on BioCoRE (in BioFS for the NAMD public project) and including the location in your message. NAMD-L will not distribute messages larger than 40K. If you can't find space for it on a webserver, we don't have space for it in our inboxes. Attached files expand in size when encoded as text by your mail client. If you are not familiar with molecular dynamics simulations you should work through the tutorials and seek assistance from a local expert.

  7. Gather, in a single directory, all input and config files needed to reproduce your problem.

  8. Run once, redirecting output to a file (if the problem occurs randomly do a short run and include additional log files showing the error).

  9. Tar everything up (but not the namd2 or charmrun binaries) and compress it, e.g., "tar cf mydir.tar mydir; gzip mydir.tar". Please do not attach files individually to your email message as this is error prone and tedious to extract. The only exception should be the log of your run showing any error messages.

  10. For bug reports, mail namd@ks.uiuc.edu with:
    • A synopsis of the problem as the subject (not "need help", "URGENT", "NAMD", or "need urgent NAMD help!!!").
    • The NAMD version, platform and number of CPUs the problem occurs with (to be very complete just copy the first 20 lines of output).
    • A description of the problematic behavior and any error messages.
    • If the problem is consistent or random.
    • A complete log of your run showing any error messages.
    • The URL of your compressed tar file on a web server.

  11. We'll get back to you with further questions or suggestions. While we try to treat all of our users equally and respond to emails in a timely manner, other demands occasionally prevent us from doing so. Please understand that we must give our highest priority to crashes or incorrect results from the most recently released NAMD binaries.