[gmx-users] Diferent ensambles for monolayers dynamics

[David van der Spoel]

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).


> 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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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,          75124 Uppsala, Sweden
phone:  46 18 471 4205          fax: 46 18 511 755
spoel at xray.bmc.uu.se    spoel at gromacs.org   http://xray.bmc.uu.se/~spoel
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