[gmx-users] Diferent ensambles for monolayers dynamics

[David van der Spoel]

On Mon, 2004-11-29 at 13:14 +0100, 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
You can just use anisotropic scaling in X and Y. Sorry, I'm not going to
read that paper...


> 
> >  
> >
> >>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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