As Steve suggests, compute msd is a good place to start. As an alternate to the fix ave/time, if you are only interested in the 4th value, the total squared displacement, you can output that with thermo_style custom c_ID[4] from your lammps input script and then pull it out of your log file with log2txt.
However, to my knowledge, no pizza.py or vmd post processing tools are available (that would for example average over multiple time origins).
-Greg
2011/1/26 <[email protected]>