[gmx-users] Question about water freezing when in contact to a solid surface (ramon)

Sun Dec 21 15:41:49 CET 2014

Hi,

It may help to use stochastic dynamics, rather than normal MD.

Cheers,

Tsjerk

On Fri, Dec 19, 2014 at 4:13 PM, André Farias de Moura <moura at ufscar.br>
wrote:
>
> Dear Ramon,
>
> I'd guess your situation is far more severe than mine, as I had a graphene
> substrate covered by chloroform, both of which have weakly attractive
> interactions as compared to silica and water, so I cannot help you further
> with that.
>
> You should realize that any solvent at solid interfaces always becomes more
> orderly and molecules slow down (several atomistic simulations have
> reported that behavior over the last decade) but CG force fields lack many
> degrees of freedom and thus they have a much smaller configurational
> entropy. For instance, a single water bead in MARTINI correspond to four
> water molecules, then the four molecules might become arranged in many
> different ways for atomistic models whereas the water beads have only the
> translational degrees of freedom. So unfortunately this is an intrinsic
> drawback and it gets worse for the more attractive potentials.
>
> best,
>
> Andre
>
> On Fri, Dec 19, 2014 at 10:39 AM, ramon <reigada at ub.edu> wrote:
> >
> > Dear Andre,
> >
> >    thank you very much for your response.
> > I tried to follow your recommendation but unfortunately I did not succed
> > and water becomes frozen anyway.
> >
> > Some details about what I am doing. I am using Gromacs v4.5.5 and Martini
> > force field.
> > I build a 20x20x12.6 nm^3 box with 7444 water molecules (W & WF)). A 15%
> > of these molecules are WF molecules (anti-freeze).
> > I minimize the system properly.
> > Later I add at z=0 a surface of Na particles. In order to cover the
> > 20x20nm^2 of the x,y plane I place 6645 particles in a planar cubic
> > configuration.
> > A randomly change a 10% of these particles to NaF new type of particle.
> > The interaction between Na and NaF particles is null. and the interaction
> > between Na and P4 and BP4 molecules is the usual in Martini force field.
> > The NaF is defined in the itp file but I use sigma=0.55 (larger beads)
> and
> > I reduce in one degree the attraction to water beads (from epsilon=4,
> semi
> > attractive, to epsilon=3.5, intermediate).
> >
> > The system is then simulated at 310K and x,y-periodic conditions without
> > any P-coupling.
> > Na and NaF particles are frozen at z=0.
> >
> > After a few iterations the first 2-3 layers of water become ordered in z
> > and almost ordered in x,y. An later, such ordering spreads up in the
> > simulation box. During this process, most WF molecules are pushed to high
> > z, far from the frozen water region close to the surface.
> > Actually, minimization once the surface is placed at z=0 already shows
> > ordering of the forst 1-2 layers. I tried to avoid such initial ordering
> by
> > setting a 2nm initial gap between the surface and the water, but the
> > simulation still gives the some behavior.
> >
> >   may be you could help me. Thanks a lot,
> >
> >    Ramon
> >
> >
> > >
> > > Date: Tue, 16 Dec 2014 16:06:07 +0100
> > > From: ramon <reigada at ub.edu>
> > > To: gromacs.org_gmx-users at maillist.sys.kth.se
> > > Subject: [gmx-users] Question about water freezing when in contact to
> > >       a       solid surface
> > > Message-ID: <4E1E1DD3-BDFF-4B5D-9035-D5B3129EF5CB at ub.edu>
> > > Content-Type: text/plain; charset=utf-8
> > >
> > > I am simulating a solid surface in contact with a slab of water and I
> am
> > using the MARTINI force field.
> > > The surface is simulated by a regular array of "Na" bead particles at
> > z=0 whose motion have been frozen.
> > > The water slab is placed on the top of the surface and the simulation
> is
> > run at 310K, no pressure coupling
> > > and periodic boundary conditions in the x,y pane.
> > >
> > > The problem is that after some nanoseconds, the water particles close
> to
> > the surface become frozen and
> > > show a regular organization that spreads to longer distances form the
> > surface until the whole aquous
> > > phase becomes frozen.
> > >
> > > I am using different amounts of WF (antifreeze water particles): 15%,
> > 20%, 25% and 30%, and water freezing
> > > appears in all cases. Any suggestion to avoid freezing in these
> > simulations?
> > >
> > > thanks for your answers,
> > >
> > >  Ramon Reigada
> > > University of Barcelona
> > > reigada at ub.edu
> > >
> > >
> > >
> > > Message: 4
> > > Date: Tue, 16 Dec 2014 19:19:47 -0200
> > > From: Andr? Farias de Moura <moura at ufscar.br>
> > > To: ramon <reigada at ub.edu>,   Discussion list for GROMACS users
> > >       <gmx-users at gromacs.org>
> > > Subject: Re: [gmx-users] Silica monolayer with Martini force field
> > > Message-ID:
> > >       <CAKTwKgpC79=YD86uK-1i4=
> > M13sWWGcX++MZ8OybcP2y0hps3GA at mail.gmail.com>
> > > Content-Type: text/plain; charset=UTF-8
> > >
> > > Dear Ramon,
> > >
> > > please keep the discussion within the list, so other people with
> similar
> > > issues may benefit as well.
> > >
> > > solvent freezing on idealized solid surfaces is an issue for CG in
> > general
> > > and MARTINI in particular. We had no success with antifreeze particles
> so
> > > we devised a protocol to render the solid substrate less idealized, by
> > the
> > > introduction of a small fraction surface defects which are
> simultaneously
> > > larger than the regular surface sites and less attractive with respect
> to
> > > the solvent (a full description of the protocol may be found in the
> ASAP
> > > version of our paper:
> > >
> >
> http://pubs.rsc.org/en/content/articlelanding/2014/cp/c4cp03519d#!divAbstract
> > > ).
> > >
> > > I hope it helps.
> > >
> > > best regards,
> > >
> > > Andre
> > >
> >
> >
> >
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> --
> _____________
>
> Prof. Dr. André Farias de Moura
> Department of Chemistry
> Federal University of São Carlos
> São Carlos - Brazil
> phone: +55-16-3351-8090
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-- 
Tsjerk A. Wassenaar, Ph.D.