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

[Sapna Sarupria]

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.

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
>>
>>
>>
>>
>>