[gmx-users] Graphene Sheet Rolling up into CNT

[Justin A. Lemkul]

Darrell Koskinen wrote:
> Hey GROMACS Gurus,
> I was wondering if you could enlighten me. I performed a simulation of a 
> graphene sheet in an ammonia gas at 240K using ffoplsaa parameters and 
> see that the graphene sheet begins to curl up into what appears to be a 
> nanotube. I did not run the simulation long enough to actually see it 
> form a nanotube, but it appears to be headed in that direction. I am not 
> sure if a graphene sheet would actually curl up on itself to form a CNT 
> at this temperature. I believe CNTs are formed by ablation of pure 
> graphite and therefore rolling up a graphene sheets must occur for the 
> CNTs to form, but assumed that the local temperature increase resulting 
> from the ablation was the cause of the rolling up. So I am wondering if 
> you might be able to give me some idea of why this is happening? Could 
> it be that the OPLS LJ parameters, since OPLS was created for liquids 
> and not gases, are creating forces too great for a gaseous simulation 
> thus causing too great an attraction between distant carbon atoms within 
> the graphene lattice, which manifests itself in the rolling up of the 
> graphene into a CNT? Or could the curling up be occurring because the 
> graphene sheet is free floating in space as would happen during 
> ablation. Maybe rolling up of graphene sheets does occur at such a low 
> temperature. I will do some research on this possibility, but in the 
> mean time please provide me your comments, if you can.
> 

My guess would be that the curling is a result of an inadequate model.  Several 
things come to mind, although probably a few of them have been discussed at some 
point in the past.

1. Appropriate use of improper dihedrals.  You shouldn't get crazy bending or 
curling if the impropers are doing their job.

2. Are you using a finite graphene sheet?  I think a better model would be an 
infinite lattice (a periodic molecule).  You might get some flexing, but you 
definitely won't get curling, if treated properly.

3. The fact that you are simulating in the gas phase.  If the ammonia is not 
close to the graphene sheet, then the graphene may only "see" itself (depending 
on how your cut-off's are set up) and therefore be spuriously attracted to itself.

-Justin

> Thanks.
> 
> Darrell
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-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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