[gmx-users] Diferent ensambles for monolayers dynamics

Hector Mrz-Seara Monne hseara at netscape.net
Mon Nov 29 12:05:44 CET 2004

Hi all,

We are simulating monolayers. Our system is based in the next configuration:


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.

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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