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VMD on Biowulf

VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. VMD supports computers running MacOS-X, Unix, or Windows, is distributed free of charge, and includes source code. VMD is closely integrated with NAMD.

VMD is developed and maintained at the University of Illinois, Urbana-Champaign. VMD website

On Biowulf, VMD is best used to display and interact with a running NAMD simulation.

There are several ways to run VMD while accessing your Biowulf data.

  1. Mount your Biowulf /data directory on your desktop system, and run VMD locally on your desktop against that data. In most cases, this will be the most efficient way to use VMD if your Mac, PC or Linux system has sufficient memory resources.
    • Follow the instructions to mount your Biowulf /home, /data or Helix /home directories on your local system. Note that this will work for Windows, Linux, and Mac desktops, but not for SGIs.
    • Download VMD from the VMD website and install on your local system. VMD is available for Windows, Linux, Mac, several other platforms, and as source code.
    • Run VMD locally against your mounted /data files.
  2. Run VMD on Helix and access your files in your /data directories. Helix has greater memory resources than the Biowulf head node, but like the head node you will not get very good visualization performance since the graphics need to be displayed across the network rather than on your local machine.
    • From your desktop, make sure you have Xwindows running, and then connect to using 'ssh -X'.
    • You can now type 'vmd' and access your NAMD files in /home/user, or /data/user.
  3. Run VMD on the Biowulf head node. This is ONLY to be done if you are using very little cpu or memory, as otherwise you could impact other users and the stability of the system.
    • From your desktop, make sure you have Xwindows running, and then connect to using 'ssh -X'.
    • On the Biowulf head node, type 'vmd'.
Useful tip: The entire PDB structural data archive is mirrored on all the systems in the area /pdb/pdb. Corresponding sequences are in /pdb/sequences/. The structural data is divided into directories named with the middle two letters of the PDB code. Thus, the data for 1crn is in /pdb/pdb/cr/pdb1crn.ent.gz