[gmx-users] Diferent ensambles for monolayers dynamics
Andre Farias de Moura
andre at qt.dq.ufscar.br
Wed Dec 1 12:01:48 CET 2004
hi hector,
On Wed, 1 Dec 2004, Hector Mtz-Seara wrote:
> Thanks Andre, for your answer, but only one more short question the
> presence of vacuum doesn't affect in the result of the surface tension
> as is calculated in gromacs as it uses de z box size,Lz? and in wich
> units are the result because it give me numbers up to 3000 for my system
> which I can't compare with experimental ones?
as a matter of fact, vacuum is necessary to create an interface,
otherwise the interaction in the z direction would affect the
pressure components in that direction, thus changing the surface
tension. as long as the void space width is larger than the
interaction cutoff it doesn't matter how large it is.
g_energy gives surface tension in bar nm, divide by 10 to get it
in mN/m (don't forget to divide by 2 as well because you have two
interfaces)
>
> My e-mail is: hseara at netscape.net for the paper
>
> Thank you, 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,
> >
> >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 Mart?nez-Seara Monn?
> >>>>>>
> >>>>>> Universidad de Barcelona
> >>>>>> Dept. Qu?mica Fisica
> >>>>>>
> >>>>>> hseara at netscape.net
> >>>>>>--------------------------------------------------------------------------------------------
> >>>>>>
> >>>>>>
> >>>>>>
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> >>>>>>
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