All pre-3.3 users can load a VMD file created with version 4.0 (and later) and vice-versa (i.e. save any VMD file with 3.2 and open it in 4.0), and
All pre-3.3 VMDs also open much faster in version 4.0 and later than in 3.3. This was improved by changing the internal file format that Chameleon is saved in to an earlier format, resulting in faster serialization.