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

[David van der Spoel]

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