[gmx-users] Re: Water spreading on graphene!
sapna.sarupria at gmail.com
Sun Apr 21 17:21:03 CEST 2013
Dear David, Vitaly and all,
Thanks for the thoughts/comments. There are no partial charges on the
carbons in this sheet. (Sorry if there was any confusion about this).
I used gromacs_4.5.5 version for these simulations. I also did increase the
graphene sheet size to 10 nm x 10 nm and the box size to have 4142 water
molecules. Initially the drop is placed about 3-4 nm away from the graphene
sheet. In 600 ps the drop moves towards the sheet (forming something that
looks like a pillar of water) and begins to spread on the sheet. The setup
itself is placed in a 20 nm x 20 nm x 20 nm box. So both big sheet, and big
box do not seem to help.
The interesting part is I have another set of simulations with silica
surface. The partial charges are turned off to make it hydrophobic. In this
case the droplet remains a droplet. The mdp files are the same - I am using
PME and NVT system with the drop and sheet coupled to different
thermostats. The silica surface is frozen (so t_ref = 0 for the sheet). I
have tested this system for gromacs 4.0.5, and 4.5.5. In both cases it
remains a droplet.
The only difference in the two is that in case of silica surface the
surface is periodic, while graphene is a finite size sheet. Does this make
such a big difference?
Thoughts, comments, suggestions welcome!
On Sun, Apr 21, 2013 at 6:39 AM, Dr. Vitaly Chaban <vvchaban at gmail.com>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.
> If you need a simple advice, it is -- enlarge the box to avoid any
> interactions, which you would not have had in real experiment.
> 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
> > 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
> > 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
> > my mdp and top file. Briefly, I am doing NVT simulation, PME for
> > electrostatics, TIP3P water model, the surface is frozen and
> > interactions are excluded, the cut-off distances are 1 nm, velocity
> > 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
> > 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!!
> > for being helpful always.
> gmx-users mailing list gmx-users at gromacs.org
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> * Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
Department of Chemical and
128 Earle Hall
Clemson, SC 29634
More information about the gromacs.org_gmx-users