[gmx-users] Diferent ensambles for monolayers dynamics

[Hector Mrz-Seara Monne]

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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>>    
>>

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