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
I have a graphene like surface (carbons on a hexagonal lattice with zero
partial charges and some LJ parameters) with a drop of water placed on it.
In principle, this is a hydrophobic surface and the drop should remain a
droplet on it. However, surprisingly I am seeing that the drop is spreading
within a 1 ns of the simulation. In the past I have done some similar
simulations (with a different structure but basically zero partial charge
surface and LJ) on which the drop remains a drop.
Does any body have any ideas of what I may be doing wrong? Pasted below is
my mdp and top file. Briefly, I am doing NVT simulation, PME for
electrostatics, TIP3P water model, the surface is frozen and intra-surface
interactions are excluded, the cut-off distances are 1 nm, velocity rescale
thermostat (I tried both with the entire system coupled to the same
thermostat and with sheet and water being coupled to different
thermostats).
Any suggestions are welcome.
My analysis suggests this comes from the long range electrostatics because
we have tested the same thing in LAMMPS. When we turn off PPPM and use
cut-off based Coulomb (~5 nm) in LAMMPS (yes now we have changed the
software) we don't see the drop spreading.
I have done so many simulations and to have this problem stumps me!! Thanks
for being helpful always.
--
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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