Hi Raouf,
Have you tried doing deformations in a more continuous way by using the "fix deform" command? This will strain your system in whatever kind of way you want.
The "fix deform" works fine with the "fix npt" - just control the pressure in the unstrained directions, so that they can respond to the strain in a natural way. This requires a system that is periodic in the straining direction and the direction(s) where you want to control the pressure.
I had a lot of problems regarding pressure, because I had made bad choices of "tdamp" and "pdamp" parameters in the "fix npt" command. Read the documentation carefully to get good advices and do tests on small systems to check if it behaves the way you want it to.
Sincerely,
Christer H. Ersland.