I thought I had given enough info. My question was regarding to the versions of compilers / mpi libraries.
Indeed, I have compiled already charmm using mpich2 (intel compilers version 9.0, mpich2 1.0.5) It kind of works, whit a speed improvement of nearly 3x under certain conditions.
But I was waiting before posting here what I did because following Rick's advice, that you reproduce, I also compiled charmm using the SGI MPI libraries (in fact, Intel MPI) The compilation was fine, no errors. But I haven't been able to test the binary, because there was an issue with the module (arsess) that is required to launch array sessions in the Altix. Our system manager has been on holidays till next Monday. Hopefully, we'll deal with the problem and then I'll post here the results and possibly new, more especific, questions.