[gmx-developers] Intermolecular parameters for graphene

[Alex]

Hi there,

Sorry, I do not have institutional access to this journal.
As a general comment, I am not at all doubting that there is work on the
subject of developing Morse-like, or any other popular potential forms. For
instance, the standard bond-order potential is also of the Morse type with
bond coordination terms. Of course,the work you mentioned could be used as
basis (additional to what I cited) for parameterizing the FFs already
implemented within GROMACS).

As far as I know, no bonding (intramolecular) interactions in GROMACS are
based on Morse-like expressions. As of right now, people who want to do
large-scale simulations of graphene or BN just go to LAMMPS, and those who
want to do biomolecular simulations involving those membranes within
GROMACS, are sort of out of luck. I am just generally hoping there's some
interest on your end in actually having something built-in. I am not really
here to promote my paper, I just like GROMACS. :)

Also, could someone rename the thread subject? I really meant
intramolecular (bonding) interactions.

Thanks,

Sasha


On Wed, Nov 19, 2014 at 1:07 AM, Gerrit Groenhof <ggroenh at gwdg.de> wrote:

> Hi,
>
> THere has been some work done on FF parameterization recently by the
> Grater group, see:
>
>
> http://pubs.rsc.org/en/content/articlelanding/2014/cp/c3cp55340j#!divAbstract
>
> Gerrit
>
>
> 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, 121405 R
> 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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