On Wed, Dec 11, 2013 at 3:39 AM, Atila Petrosian

> Dear Justin
> Thanks for your reply.
> After energy minimization, all carbon atoms are in true position,
> inside box but again, both ends of cnt were deformed, same problem I
> had before I add bond length to the length of CNT in z dimension of box.
> You mentioned " possibly poor input geometry ". Please tell me how to
> obtain better input geometry.
Well, you haven't said how you're building the CNT, so there's nothing I
can suggest.  It was just sort of a random guess, anyway - initial
coordinates being bad (for whatever reason) is one common source of

> I confused. How to solve this problems?

It's also possible that your force field is bad or that the box is still
incorrectly sized, depending on the geometry of the CNT.




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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