Rosetta ab initio run gives 0.00 RMSD for generated 2000 models? (run still in progress)
RMSD is a measure of similarity between two structures. The relevant RMSD in protein structure prediction is between a model and the native structure. If you don't have a native structure you cannot have an RMSD in this sense. Ignore the fact it is 0.0, there is possibly some error that means you are calculating the RMSD between a model and itself.

And that's the difficulty of protein structure prediction... you don't know whether you are right or not! The structures you have generated are your results, and you'll need to find ways to filter or use them that are not reliant on RMSD. You could use estimation of model accuracy methods or clustering, for example.