On Tue, Dec 10, 2013 at 4:02 AM, Atila Petrosian
<atila.petros...@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?
>

Looks like normal PBC, but possibly poor input geometry.  Does energy
minimization lead to a (visually) better state?

-Justin

-- 

==========================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441


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