[gmx-users] Diferent ensambles for monolayers dynamics

[Andre Farias de Moura]

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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