[gmx-users] Diferent ensambles for monolayers dynamics
David van der Spoel
spoel at xray.bmc.uu.se
Mon Nov 29 13:03:51 CET 2004
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
> --------------------------------------------------------------------------------------------
>
>
>
> _______________________________________________
> gmx-users mailing list
> gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-request at gromacs.org.
--
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
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
More information about the gromacs.org_gmx-users
mailing list