VMD - A Package for Visualizing Molecules
Motivation and Suggestion that VCL is a good way to run VMD
The VMD package is supported from the University of Illinois NCSA as part of the NIH bioinformatics software effort. VMD allows visualization and some manipulation of rather complicated biological molecules, which can be entered in a variety of formats. It can be used in conjunction with the NAMD software to observe simulations of molecular vibrations over femto (1.e-12) second scales.
If VMD jobs execute sluggishly on the headnode or if you want to do an extended session, it's a good idea (and polite to your fellow users) to work from a VCL node. In that case, go to http://vcl.ncsu.edu and select an HPC Linux node.
VCL gives you exclusive access to a node for up to 4 or 6 hours, whereas on the login nodes you're sharing a node with as many others as happen to be logged in at that time. When a couple of users simultaneously use the login nodes for computation, they grow sluggish and sometimes lock up, necessitating reboots, loss of user sessions, and pentance from the offending users.
Using VMD and VMD Tutorials
After logging into a VCL node, type:
at the command line. For some tutorials and example codes for using VMD, see VMD tutorials. Available tutorials show how to use VMD with Amber, VASP, and NAMD. From this same site, you can also download VMD for installation on your own PC (Linux, Mac, and Windows binaries are available).
Using the VMD GUI on Windows
To get the graphical user interfaces for VMD on Windows using XWin-32 and putty may require an additional step to get the OpenGL library (compared to the usual procedure to get an X-Window).
Right click on the XWin-32 button and go the Xconfig. Open the Other tab. Depending on the version of X-Win32, check the box labeled OpenGL Software Rendering .. or the box labeled GLX Buffering. Then restart X-Win32.
As usual when using putty, go to the ssh tab, and make sure X11 tunneling is "on". On some versions of putty, this is under "tunneling". This allows you to get an X-Window on the HPC VCL image. You can check whether you can get a X-Window by typing:
at the command line.
Windows, Linux, and other versions of VMD are available for free download from Download VMD.