I have uploaded 1ubq.pdb into the VMD software. I then went through the steps laid out on the NAMD tutorial prepared by the University of Illinois. During one of the later stages of the tutorial (http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/node10.html), I am required to type "./namd2 ubq_wb_eq.conf > ubq_wb_eq.log &" into the MS-DOS command window that comes with the NAMD/VMD software. I have already solvated the ubiquitin molecule in a water box. When I type the command that I have just mentioned, the software SHOULD run the simulation. Now, I am COMPLETELY new to biocomputation and my question may seem bizarre to you all, but I have to ask. When the tutorial says
Run your simulation by typing in a terminal window
./namd2 ubq_wb_eq.conf > ubq_wb_eq.log &
should I not be able to see the molecule in the VMD OpenGL Display window? There is NOTHING happening in my VMD OpenGL Display window. All that happens when I type in that command into the MS-DOS command window is that a bunch of new files are created in my 1-3-box folder, and these files are called ubq_wb_eq.dcd, ubq_wb_eq.restart.coord, ubq_wb_eq.restart.vel.old, etc etc etc. The bottom line is, many files are created when I type in that command into the terminal window, but there is no simulation (i.e. visual simulation of the ubiquitin in a water box). Can someone please tell me what is the point of "simulation" when all you get is a bunch of files that makes no sense but you don't get to see any molecules in the display window?
