[gmx-users] Diferent ensambles for monolayers dynamics

[Andre Farias de Moura]

hi hector,

On Wed, 1 Dec 2004, Hector Mtz-Seara wrote:

> Thank you very much Andre, my system has two monoloyers one on each
> side. Do you think that the way of calculate surface tension of gromacs
> is accurate enough I haven't found so much information about how it's
> evaluated inside the package, if not how do you make the measure?
> In advance hundreds of thanks was very useful your answer.

I wouldn't say it's accurate, pressure calculations are inherently
noisy, very noisy, but g_energy uses standard procedures to calculate
the surface tension from energy output (take a look at the manual in
the surface tension coupling section). although noisy, average values
are consistent if your simulations are properly set up.

>
> ( have you any paper with your isotherms????)
>

I've just submitted a paper to the J. Physical Chemistry, I'll send
you a copy as soon as it's into final form.

> Hector
>


best regards,

andre'

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

    Dr. Andre' Farias de Moura

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

  Laboratorio de Quimica Teorica
Universidade Federal de Sao Carlos
     Sao Carlos - SP - Brasil

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/

        Endereco Atual

    Grupo de Quimica Quantica
Instituto de Quimica de Sao Carlos
    Universidade de Sao Paulo
    Sao Carlos - SP - Brasil
    Telefone: 55-16-3373-8055

/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/


>
>
> Andre Farias de Moura wrote:
>
> >Hi Hector,
> >
> >I couple of months ago I posted a message saying that NVT
> >was OK to simulate monolayers but it seems to me now that
> >there may be some regions in lipids isotherms where non-
> >equilibrium (metastable) states occur. surface-tension is
> >certainly a better coupling than NVT for monolayers, you
> >just need to set compressibility to zero in the direction
> >perpendicular to the interface to avoid the system
> >collapse you mentioned.
> >
> >by the way, if I understood your system setting, you're
> >using only one lipid monolayer on one side of the water
> >slab, the other side being a water/vacuum interface. it
> >seems to me that you should use one monolayer on each
> >side of the water slab, see the work of Ahlstrom and
> >Berendsen J. Phys. Chem. 97 (1993) 13691. if you don't,
> >your surface pressure will have both a water surface
> >tension contribution and the water/lipid interfacial
> >tension, I don't think that these contributions can be
> >separated.
> >
> >I hope it helps,
> >
> >best regards,
> >
> >andre'
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >    Dr. Andre' Farias de Moura
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >  Laboratorio de Quimica Teorica
> >Universidade Federal de Sao Carlos
> >     Sao Carlos - SP - Brasil
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >        Endereco Atual
> >
> >    Grupo de Quimica Quantica
> >Instituto de Quimica de Sao Carlos
> >    Universidade de Sao Paulo
> >    Sao Carlos - SP - Brasil
> >    Telefone: 55-16-3373-8055
> >
> >/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/-/
> >
> >On Mon, 29 Nov 2004, Hector Mrz-Seara Monne wrote:
> >
> >
> >
> >>spoel at xray.bmc.uu.se wrote:
> >>
> >>
> >>
> >>>On Mon, 2004-11-29 at 12:05 +0100, Hector Mrz-Seara Monne wrote:
> >>>
> >>>
> >>>
> >>>
> >>>>Hi all,
> >>>>
> >>>>We are simulating monolayers. Our system is based in the next configuration:
> >>>>
> >>>>               VACUUM
> >>>>               ------
> >>>>               LIPID
> >>>>               ------
> >>>>               WATER
> >>>>               ------
> >>>>               VACUUM
> >>>>
> >>>>in the literature we have found two mainly different ensembles to work with monolayers simulations,
> >>>>the first NVT which works perfectly and the second NPnT( surface tension ) which in our simulations the
> >>>>vacuum disappeared because the Berendsen pressure algorithm scales the box till the box surrounds
> >>>>perfectly the system without vacuum,after a few dynamic steps, which means that we have interaction of
> >>>>the lipids and the water across the box by the periodic boundary conditions.
> >>>>
> >>>>
> >>>>
> >>>>
> >>>>
> >>>You only should scale the X en Y coordinates of the box (in the plane of
> >>>the lipids).
> >>>
> >>>
> >>>
> >>>
> >>>
> >>Then it means that you can't use NPnT( surface tension ) ensemble and
> >>the correct one is NVT or NA( surface tension )T, it is
> >>correct or there is something that I'm not understanding? It's just that
> >>the article that I mention confuses me
> >>
> >>
> >>
> >>>
> >>>
> >>>>The problem is that in the article, Biophysical Journal;Volume 82;2511-2519, it seems that Dr. Feng Sun
> >>>>is using the second ensemble without loosing the vacuum because he uses periodic boundary conditions, and
> >>>>water and lipids do not interact across the box. The package he use is charm. Someone knows if the algorithm
> >>>>of Charmm for the pressure bath is different from gromacs's one and don't scale the box the box, allowing you
> >>>>to have vacuum in both sides of the monolayer while normal pressure, Pn, is applied to the bulk system. If not
> >>>>how anyone can use NPnT(surface tension) ensemble for simulating monolayers? Is correct to use NVT ensemble
> >>>>in order to build an isotherm?
> >>>>
> >>>>Thank you, Hector
> >>>>
> >>>>--------------------------------------------------------------------------------------------
> >>>>               Hector Martínez-Seara Monné
> >>>>
> >>>>                    Universidad de Barcelona
> >>>>                         Dept. Química Fisica
> >>>>
> >>>>                          hseara at netscape.net
> >>>>--------------------------------------------------------------------------------------------
> >>>>
> >>>>
> >>>>
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