[gmx-users] Silica monolayer with Martini force field

[André Farias de Moura]

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

On Tue, Dec 16, 2014 at 1:12 PM, ramon <reigada at ub.edu> wrote:
>
> Dear Andre,
>
>    you helped me a lot with your advises about how to built an alkane
> monolayer attached to a solid surface (see your attached email).
> I succeded with my simulations, except for the case when the surface is
> free from alkane or the alkane is short and not too dense.
> In these cases, the water freezes and the simulations have no sense at all.
> 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.  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?
>
> thank you again for your help,
>
>   Ramon Reigada
> University of Barcelona
> reigada at ub.edu
> El 29/10/2014, a las 15:05, André Farias de Moura escribió:
>
> > Dear Ramon,
> >
> > we did something like that last year, except that our system was a ZrO2
> > nanoparticle and the chains were carboxylic acid instead of alkanes, but
> > the ideas are similar:
> >
> > Nanocrystals self-assembled in superlattices directed by the
> > solvent–organic capping interaction, Nanoscale 5 (12), 5602-5610, 2013.
> >
> > I would summarize as follows:
> >
> > (1) if the grafting density is high (say, nearly 100% surface sites are
> > covered) and chain length is large enough (say, 3-4 beads), then the
> direct
> > interaction of the solvent with the solid substrate is neglible, because
> > surface becomes protected by a dense organic monolayer.
> >
> > (2) the fact that alkanes are going to be exposed to water will lead to a
> > very high interfacial energy and this will be the dominant interaction
> > defining the packing of the hydrocarbon chains (the so-called hydrophobic
> > effect), not the weak, attractive dispersion interaction between alkyl
> > chains and the substrate or between alkyl chains, so again the
> interactions
> > involving the solid are not so important.
> >
> > in short, I think you may set a polar site to the glass units and freeze
> > them and then check if these assumptions hold in your simulated system.
> >
> > (which polar site to choose depends on the properties of the glass you
> are
> > interested in: if you have contact angle data for the glass-water and
> > glass-alkane you might in principle choose the best parameters)
> >
> > I hope it helps.
> >
> > best,
> >
> > Andre
> >
> > On Tue, Oct 28, 2014 at 5:22 PM, RAMON REIGADA SANZ <reigada at ub.edu>
> wrote:
> >
> >> Hi Gromacs users,
> >>
> >>   I want to simulate a monolayer of alkane molecules attached to a solid
> >> glass surface. I wonder if anyone has experience with these kinds of
> >> systems with the Martini force field. My idea is to add water to the
> >> surface and I am interested in what happens between water and the fixed
> >> alkanes, so I will freeze the solid beads and the first carbon of the
> >> alkane chain.
> >> My question is what kind of beads would correspond to glass (silica)
> >> surface? Somewhere I found that 'Na' beads could be used to simulate a
> Pt
> >> surface, but I do not know if this would work in my case.
> >> Did anyone has experience simulating solid surfaces with Martini?
> >>
> >>  thank you,
> >>
> >>  Ramon
> >>
> >>
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> >>
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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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>
> 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.
>
>

-- 
_____________

Prof. Dr. André Farias de Moura
Department of Chemistry
Federal University of São Carlos
São Carlos - Brazil
phone: +55-16-3351-8090