Justin A. Lemkul wrote:
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.
Agreed, and perhaps the sheet is too thin to behave like bulk graphite.
Certainly a single layer will not have (all) the properties of graphite.
Mark
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