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Hoi Alessio,

you are right and Daniele is also right. Try 

   root [0] gSystem->Load("libPhysics.so");
   root [1] gSystem->Load("./libNtuples.so");
   root [2] 

It might be useful to put the libPhysics.so loading into your
rootlogon.C. 

Cheers,
--U.