<p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;">Hi Tsjerk,</p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><br></p><p style="border:0; padding:0; margin:0; font-family:'Gulim'; font-size:10pt; cursor: text;"><span style="font-size: 12px; line-height: 18px;">> Do you have experimental data on the behaviour of 2000 or 6000 or 10000</span></p><pre style="font-size: 12px; line-height: 18px;">> water molecules on a sheet of graphene? </pre><pre style="font-size: 12px; line-height: 18px;">There are experimental and theoretical data that describe the contact angle of water on graphene. </pre><pre style="font-size: 12px; line-height: 18px;"></pre><pre style="font-size: 12px; line-height: 18px;"><pre>Current experimental data of water droplets on a sheet of graphene can be found in the work by</pre></pre><pre style="font-size: 12px; line-height: 18px;">Rafiee et al., Nature Materials Vol. 11 217-222 (2012), </pre><pre style="font-size: 12px; line-height: 18px;">Li et al., Nature Materials Vol. 12 925-931(2013), </pre><pre style="font-size: 12px; line-height: 18px;">and Zhou et al., Phys. Rev. B 85, 035406 (2012).</pre><pre style="font-size: 12px; line-height: 18px;"><br></pre><pre style="font-size: 12px; line-height: 18px;">Theoretical calculations of the 2000, 6000, and 10,000 molecules have also been reported by </pre><pre style="font-size: 12px; line-height: 18px;">Shih et al., Nature Materials (Commentary) Vol. 12 866-869 (2013),</pre><pre style="font-size: 12px; line-height: 18px;">Shih et al., PRL 109, 176101 (2012),</pre><pre style="font-size: 12px; line-height: 18px;">and Taherian et al., Langmuir 29, 1457-1465 (2013), just to name a few.</pre><pre style="font-size: 12px; line-height: 18px;"><br></pre><pre style="font-size: 12px; line-height: 18px;">> Do you _know_ it's wrong behaviour?</pre><pre style="font-size: 12px; line-height: 18px;"><pre>Since I am new to gromacs calculations, I am afraid I do not know what went wrong with the calculation. </pre><pre>Either the effect of polarisation makes the surface superhydrophilic, or the neighbouring interaction prevents water from forming a droplet.</pre><pre>Water should, however, form a droplet on the surface.</pre><pre><br></pre><pre>> 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.</pre><pre>> Where did those parameters come from?</pre></pre><pre style="font-size: 12px; line-height: 18px;">GRAPPA force field (Hughes et al., Nanoscale 6, 5438-5448 (2014)) was developed based on CHARMM FF, where the FF parameters were </pre><pre style="font-size: 12px; line-height: 18px;">obtained through first deriving a set of C-C parameters, following by </pre><pre style="font-size: 12px; line-height: 18px;">the parameters of different oxygen-containing species.</pre><pre style="font-size: 12px; line-height: 18px;">Another similar polarisable FF was also recently developed based on OPLS/AA by Schyman and Jorgensen, J. Phys. Chem. Lett. 4, 468-474 (2013).</pre><pre style="font-size: 12px; line-height: 18px;"><pre><br></pre><pre>> Do they account for increased electron density
> above the plane because of all the pi-orbitals?</pre><pre>I am not absolutely certain that the pi-orbitals were accounted for, </pre><pre>however, the authors have described that GRAPPA can capture the overlap of pi-electron cloud between residue and graphene surface.</pre><pre><br></pre><pre><br></pre><pre>Regards,</pre><pre>Kester</pre><pre><br></pre></pre><blockquote style="font-size:12px;border-left-style:solid;border-left-width:2px;margin-bottom:0pt;margin-left:0.8em;margin-right:0pt;margin-top:0pt;padding-left:1em;"><div style="font-family:arial,돋움;line-height:1.5"><div style="margin-top:5px;"><pre>
Do you have experimental data on the behaviour of 2000 or 6000 or 10000
water molecules on a sheet of graphene? </pre><pre><br></pre><pre>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@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.
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