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.
- 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.
- 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 helix.nih.gov using 'ssh -X helix.nih.gov'.
- You can now type 'vmd' and access your NAMD files in /home/user, or /data/user.
- 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 biowulf.nih.gov using 'ssh -X biowulf.nih.gov'.
- On the Biowulf head node, type 'vmd'.
