Namd and vmd are installed in directories /usr/local/namd and /usr/local/vmd-1.8.1/ respectively.To use OpenGl graphical window of vmd,you have to set the variable DISPLAY.All therequired files for this tutorial are located in the directory /home/gsmurthy/biosim/help.You can copy them to your Directory by using scp, ie
cd /home/gsmurthy/biosim scp -r help $HOME@ncsc0: cd cd help
The results of every task performed is available in respective directories(in directory results) which can used for comparison.