The VMD source code can be obtained after registering at: http://www.ks.uiuc.edu/Research/vmd/VMDregistration.html There are also binary versions for several OSs there. After downloading the file with your web browser, uncompress and untar the file. This will produce a subdirectory named vmd-1.3. Unless otherwise specified, all references to VMD code will be from this subdirectory, so cd there.