From: Paul Grayson (pgrayson_at_ks.uiuc.edu)
Date: Wed Feb 20 2002 - 19:59:54 CST

I have a possible solution for you. VMD can act as a web server,
allowing a java program to control it simply by loading a URL like

  http://127.0.0.1:8000/load%20pdb%20fileName.pdb

You can download an example TCL script that lets you do this here:

  http://www.ks.uiuc.edu/Research/vmd/script_library/scripts/webvmd/

We wrote this script so that we could create web pages that control
VMD, but a java program should be able to do anything that your web
browser can. Let me know if you have any questions about setting up
the script!
-Paul