[gmx-users] Re: Water spreading on graphene!

[Sapna Sarupria]

Dear David,

I apologize for the confusion. There are no partial charges on the graphene
sheet . The only interactions between the sheet and water are from VdW
interactions.

To give some background:
We were initially simulating graphene oxide with water which has partial
charges. Then to test the effect of oxygens we retained the carbons and
their partial charges, and simulated the system. As expected it was
hydrophilic. Then we turned off all the partial charges to obtain a
graphene sheet and tested the system. Unexpectedly, we still saw the drop
spreading. That is how the whole mystery originated. I hope this clarifies
things.

Again, there are no partial charges on the graphene sheet.

Sapna


On Sun, Apr 21, 2013 at 1:23 PM, David van der Spoel
<spoel at xray.bmc.uu.se>wrote:

> On 2013-04-21 18:25, Sapna Sarupria wrote:
>
>> Dear David and all,
>>
>>
>> Thanks for the suggestions!
>>
>> I did increase the box size to twice that of the sheet dimensions. The
>> sheet is 10 x 10 nm^2 and now is place in the center of a 20 x 20 x 20
>> nm^3
>> box with the droplet size of about 5 nm (4142 water molecules). I still
>> see
>> the droplet spreading.
>>
>> I will check the energies and also attempt the simulation with the cut-off
>> distances. May be that will help.
>>
>> However, in a silica surface with no surface charges the drop remains a
>> drop (as expected). I use the same mdp files for both the simulations.
>>
>>  You did not explain the charges on graphene.
>
>
>  Sapna
>>
>>
>> On Sun, Apr 21, 2013 at 12:14 PM, David van der Spoel
>> <spoel at xray.bmc.uu.se>wrote:
>>
>>  On 2013-04-21 12:39, Dr. Vitaly Chaban wrote:
>>>
>>>  Yes, the water droplet should remain a droplet on graphene.
>>>>
>>>> Since you have a droplet, I assume you have much vacuum in the system. I
>>>> would not use PME for such system, but would rather "compensate" it by
>>>> using larger cutoffs.
>>>>
>>>>   It could be an artifact if the box dimension is small compared to the
>>>>
>>> droplet (less than double the droplet size, make it at least three times
>>> the droplet). In principle PME should work though. Check the energy
>>> before
>>> and after the droplet spreads to see whether the energy goes down.
>>>
>>>
>>>
>>>   If you need a simple advice, it is -- enlarge the box to avoid any
>>>
>>>> interactions, which you would not have had in real experiment.
>>>>
>>>>  Indeed.
>>>
>>>
>>>
>>>  I also expect a specific behavior, if your droplet is very small.
>>>>
>>>> Maybe, I would simulate this system without PBC at all.
>>>>
>>>>
>>>> Dr. Vitaly Chaban
>>>>
>>>>
>>>>
>>>>
>>>>
>>>>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone:  +46184714205.
> spoel at xray.bmc.uu.se    http://folding.bmc.uu.se
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-- 
Sapna Sarupria
Assistant Professor
Department of Chemical and
Biomolecular Engineering
128 Earle Hall
Clemson University
Clemson, SC 29634