[gmx-users] deformation in cnt

[Atila Petrosian]

Dear Justin


Based on your suggestion, I added C-C bond length to z dimension of box
(before: 5.5 3.5 3.5, now: 5.5 3.5 3.6418).

Then I used genion to neutralize system using replacing 2 water molecules
by 2 Na ions, gro file obtained from genion is strange.

When I see this gro file by vmd, some carbon atoms of CNT leave the  box.

Figure is in the bellow link:

https://www.dropbox.com/s/kt1xk4ps3kbxze3/cnt-pic.docx


What is reason of this issue?

How to fix it?