[gmx-users] deformation in cnt

[Justin Lemkul]

On Tue, Dec 10, 2013 at 4:02 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?
>

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

-Justin

-- 

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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

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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