[gmx-developers] Intermolecular parameters for graphene

Gerrit Groenhof ggroenh at gwdg.de
Wed Nov 19 09:07:09 CET 2014


THere has been some work done on FF parameterization recently by the Grater group, see: 



On Nov 19, 2014, at 9:41 AM, Alex wrote:

> 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. 
> Thanks,
> Sasha
> -- 
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