Need Help?

Don't forget that documentation is written to help you! If you have having issues with BrownDye or NAMD, see the links to their documentation in number 4. If you are experiencing problems with SEEKR, SEEKR's documentation is found here. If you found a bug or an issue, please post your concern on GitHub!

Download Instructions

  SEEKR was written for computers running Linux operating system. Be sure your machine is running Linux before you begin.

1. Compile BrownDye

2. Compile NAMD

  • Find the latest version of NAMD for Linux.
  • Follow the registration or login steps to download.
  • Consult the NAMD Website for full documentation if you have questions.
  • Longer simulations will be completed on TACC's Stampede, for which we have a separate version of NAMD to compile. You will get to that in SEEKR's tutorial.

3. Verify NAMD and BrownDye Have Been Compiled Correctly

  • An effective way for beginners to test their new installation of NAMD and Browndye is to complete the tutorials.
  • Work through the BrownDye tutorial.
  • Work through the NAMD tutorial.

4. Remember the Importance of Experience in MD and BD

  • SEEKR's success hinges on your knowledge of both MD and BD. Make sure you understood every step of the tutorials you completed!
  • See documentation on NAMD or BrownDye if you need to further familiarize yourself with those programs.

5. Download SEEKR from GitHub

  • Check out our GitHub.
  • Clone our GitHub directory by opening a terminal on your Linux machine.
  • Choose a directory you will clone SEEKR in. If you choose $HOME, type this into your terminal:

      cd $HOME
      git clone https://github.com/nbcrrolls/SEEKR.git

6. Work Through SEEKR's Tutorial