[gmx-developers] Intermolecular parameters for graphene

Alex nedomacho at gmail.com
Wed Nov 19 08:41:50 CET 2014

Dear developers,

I really hope to get your attention.
I may be wrong, but GROMACS still doesn't have a reasonable built-in
parameterization for graphene as part of any FF. There are some tutorials
online, but they are all quite flaky, based on the parameterizations of
organic molecules (as expected). Given the few rounds of chatting with the
reviewers I've had for my last paper on the subject, the parameterization
is sorely desired. So, maybe it could be a good idea for you to look into
it, as people do want a proper model of graphene to simulate it in water in
the presence of all the other things that GROMACS simulates so well.

For a DREIDING-like model, here are possibly useful papers containing
pretty much complete descriptions of the parameter sets:

1. J. H. Los et al* Scaling properties of flexible membranes from atomistic
simulations: Application to graphene*, Phys Rev B. 80, 121405R 2009.
(this model is parameterized by differentiating the LCBOPII bond-order
potential, which fails at describing the phonon spectrum of graphene. No
dihedral constraints, see below Fig. 1)

2. A Shakouri, T Y Ng and R M Lin *A new REBO potential based atomistic
structural model for graphene sheets *Nanotechnology 22(29), 295711, 2011.
(no dihedrals here either, based on the second-generation bond-order
potential, which fails in the harmonic spectrum)

3. A. Smolyanitsky Molecular dynamics simulation of thermal ripples in
graphene with bond-order-informed harmonic constraints, Nanotechnology
25(48), 485701, 2014.
(this is my work, the parameterization does have dihedrals, and it is based
on the phonon-optimized second-gen bond-order potential, which is described
in ref #6 of this work).

For the most part, all of these parameterizations do not directly
correspond to the "parent" potentials (except around 0 K), as spring-like
FFs will generally present a relatively stiff model, but I think this info
could be a small step forward. I hope this is useful. If you have any
questions on the numbers, please do let me know.


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