You can obtain the VMD source from ftp.ks.uiuc.edu in /pub/mdscope/vmd/ . For version 1.2b2 this is vmd-1.2b2.src.tar.gz . There are also binary versions for several OSs there (See the README file in the directory). Decompress and de-tar the file. This will produce a subdirectory named vmd-1.2b2. Unless otherwise specified, all references to VMD code will be from this subdirectory, so cd there.