I am trying to equilibrate a nanotube/polymer system. I declare the nanotube as rigid. I constraint C-H bond lengths in the matrix by SHAKE. Then I integrate the system with fix NPT aniso partial where I apply pressure constraints in x and y for the matrix alone. I did not employ constraints in z since the nanotube stays as it is eventough the nanotube does not span through the box, it is short and in the middle.
The volume of the system immediately enlarges by almost 7 times. Then it decreases only slightly. I ran my simulation for 100 ps and the volume reached to a steady level but still is huge.
I visualized the atoms. The atoms are squeezed in on corner of the big box and few atoms are on the other end due to PBC. But the relative changes of coordinates are minor. I can not explain why this happens. My initial system is in the main box will image flags all zero. When I try soft potential instead of lj/cut I have the same problem, worse this time. Any ideas why this may be happening?
Thank you for your time,