Did you had a look at this one :

http://www.ks.uiuc.edu/Training/Tutorials/namd/namd-tutorial-win-html/namd-tutorial-win.html

I have never used NAMD on windows but this tutorial seems to cover most of the things one can do.

I highly recommend you to learn how to use Linux-based systems if you are interested in molecular modeling approaches.

I agree it will definitely make your life much more easier, especially when you will have to analyze the results because I don't think that all the processing scripts/packages will be available on windows

Thanks to all