[gmx-users] Unrealistic behaviour of water on graphene [NVT]

[Tsjerk Wassenaar]

Hi Kester,

Do you have experimental data on the behaviour of 2000 or 6000 or 10000
water molecules on a sheet of graphene? Do you _know_ it's wrong behaviour?
If yes, then, given that the water forms a droplet in vacuum, even if above
the graphene sheet, you know the water behaviour itself is sort of correct.
I would be most suspicious of the water-graphene interactions. Where did
those parameters come from? Do they account for increased electron density
above the plane because of all the pi-orbitals?

Cheers,

Tsjerk


On Tue, Sep 2, 2014 at 8:24 AM, Kester Wong <Kester2014 at ibs.re.kr> wrote:

> Dear gmx-users,
>
>
> I am modelling a water droplet using a water box model, and have
> encountered unrealistic behaviour of equilibrating water on graphene, using
> GRAPPA force field in GROMACS 5.0.
>
> The box size is about 30x30x15 nm. Structure-wise, the water models (2000,
> 6000, and 10,000 water molecules) appear to be spreading like a flat
> layer of solution, rather than a droplet.
>
> Additionally, for the 10,000 molecules on graphene, water droplet was
> formed in vacuo above the surface.
>
>
> I have posted some questions on GROMACS user list, however, I have yet to
> receive any feedback.
>
> Could anyone please look at my .mdp parameter and the .xtc trajectory
> files? I do not know what caused the spreading of water on graphene.
>
>
> There are two parameter settings that I have used, they are labeled as
> lincs-order=4 (larger temperature constant and time-step), and
> lincs-order=8 (smaller temperature constant and time-step).
> The starting configuration (pdb), trajectories (xtc), and parameter (mdp)
> files are uploaded in my Google Drive:
> ​
>
>
> https://drive.google.com/folderview?id=0B7ym8d6G9-e2Tlh4VGNSaDhCbmc&usp=sharing
>
>
> https://drive.google.com/folderview?id=0B7ym8d6G9-e2Rl9WaXNrUlVRa28&usp=sharing
>
>
> https://drive.google.com/folderview?id=0B7ym8d6G9-e2bnFzbWN3VHVqbE0&usp=sharing
>
>
> Please let me know if you need more information/files on the GRAPPA-based
> calculations.
>
> Any help will be tremendously appreciated.
>
>
>
> Regards,
>
> Kester
>
>
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-- 
Tsjerk A. Wassenaar, Ph.D.