[gmx-users] Diferent ensambles for monolayers dynamics

[Hector Mtz-Seara]

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.

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

Hector



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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