[gmx-users] CNT going out of the simulation box after NVT.

[soumadwip ghosh]

 Dear users,
                   I am simulating swCNTs in the presence of nucleic acids
with finite length. I have created the topology of swCNT from the PDB I
obtained from Tubegen software. I used CHARMM all atomic force field to
build the topology for both the CNT as well as the DNA. I included the
CNT.top in the ssDNA.top by modifying atom types. I put the hybrid system
inside a box of dimension 7.46 x 3.5 x 3.5 nm3 and proceeded fro energy
minimization after charge neutralization. Energy was minimized within 500
steps in a steepest descent process. When I took the em.gro file and
visualized in VMD, portion of the DNA was found outside the box. Hence, I
did trjconv  with -center to keep the DNA in the center of the box. Then I
did another energy minimization. The em.gro file this time looked ok in
VMD. Then, I did the NVT for 1 ns . When I checked the nvt.gro file, now
the CNT is going outside the box. I cant understand why it is happening.
The DNA is supposed to wrap around the nanotube. Can anyone help me out
with this?


Thanks and regards,

 Soumadwip Ghosh
  Research Fellow
   IITB, Mumbai.
   India.