Comparing other protocols of ns2 with the protocols of Aqua-Sim

Yes.
I think, technically that kind of comparison is possible if and only if the aquasim patched version of ns-2 is not not really distrubing the integrity and working of other agents or protocols of ns-2.

But, if it technically affecting other agents or protocols after patching it for aquasim, then you may need two seperate ns-2 installations – one with default ns-2 and the another with aquasim patch.

But my advise is : For safer side, run the two set of simulations (one with default ns-2 and another with aquasim patched ns-2) separately and then compare the two results by doing custom trace analysis on the two sets of trace outputs.

Charles Pandian