[gmx-users] deformation in cnt

[Dr. Vitaly Chaban]

If the system does not explode, everything is correct. Though your
solution is perhaps in the wrong place in relation to the tube.


Dr. Vitaly V. Chaban


On Tue, Dec 10, 2013 at 10:02 AM, Atila Petrosian
<atila.petrosian at gmail.com> wrote:
> 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?
> --
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