[gmx-users] Question about water freezing when in contact to a solid surface (ramon)
André Farias de Moura
moura at ufscar.br
Fri Dec 19 16:13:09 CET 2014
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
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.
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
> 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,
> > 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
> > 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
> > and MARTINI in particular. We had no success with antifreeze particles so
> > we devised a protocol to render the solid substrate less idealized, by
> > 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:
> > ).
> > I hope it helps.
> > best regards,
> > Andre
> Aquest correu electrònic i els annexos poden contenir informació
> confidencial o protegida legalment i està adreçat exclusivament a la
> persona o entitat destinatària. Si no sou el destinatari final o la persona
> encarregada de rebre’l, no esteu autoritzat a llegir-lo, retenir-lo,
> modificar-lo, distribuir-lo, copiar-lo ni a revelar-ne el contingut. Si heu
> rebut aquest correu electrònic per error, us preguem que n’informeu al
> remitent i que elimineu del sistema el missatge i el material annex que
> pugui contenir. Gràcies per la vostra col·laboració.
> Este correo electrónico y sus anexos pueden contener información
> confidencial o legalmente protegida y está exclusivamente dirigido a la
> persona o entidad destinataria. Si usted no es el destinatario final o la
> persona encargada de recibirlo, no está autorizado a leerlo, retenerlo,
> modificarlo, distribuirlo, copiarlo ni a revelar su contenido. Si ha
> recibido este mensaje electrónico por error, le rogamos que informe al
> remitente y elimine del sistema el mensaje y el material anexo que pueda
> contener. Gracias por su colaboración.
> This email message and any documents attached to it may contain
> confidential or legally protected material and are intended solely for the
> use of the individual or organization to whom they are addressed. We remind
> you that if you are not the intended recipient of this email message or the
> person responsible for processing it, then you are not authorized to read,
> save, modify, send, copy or disclose any of its contents. If you have
> received this email message by mistake, we kindly ask you to inform the
> sender of this and to eliminate both the message and any attachments it
> carries from your account. Thank you for your collaboration.
> Gromacs Users mailing list
> * Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
More information about the gromacs.org_gmx-users