[gmx-users] Question about water freezing when in contact to a solid surface (ramon)
reigada at ub.edu
Fri Dec 19 14:41:19 CET 2014
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,
> 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
> <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:
> I hope it helps.
> best regards,
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