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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--
========================================
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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