[gmx-users] deformation in cnt

Atila Petrosian atila.petrosian at gmail.com
Tue Dec 10 10:02:58 CET 2013

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:


What is reason of this issue?

How to fix it?

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