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
<[email protected]>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.
[email protected] http://folding.bmc.uu.se
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