Re: System with two membranes

From: Giacomo Fiorin (
Date: Fri Apr 30 2021 - 10:03:41 CDT

Hi José, like Josh said, equilibrating with an anisotropic barostat is the
key (preferably constraining the ratio of the X-Y dimensions).
Additionally, although the two bilayers do have similar equilibration
times, their exact trajectories will be a bit different and the sporadic
mismatch that may occur undesirable.

If so, equilibrating each bilayer on its own and merging the two systems
*after* equilibration would be the way to go. The interface between the
two juxtaposed water layers will vanish very quickly.


On Fri, Apr 30, 2021 at 10:01 AM Vermaas, Josh <> wrote:

> Hi Jose,
> What did you do to your periodic box size in the NAMD configuration file,
> and how is the barostat allowed to change it? Normally, the x-y dimensions
> are the same between the two membranes, so you use the semi-isotropic
> ensemble options for the barostat (useflexiblecell yes, useconstantratio
> yes), and it is quickly impossible for water to cross either membrane
> without going through it. If you are getting water channels in your
> membrane, the x-y dimenstions may have been too large in the beginning, and
> the fast water diffusion formed a stable pore.
> -Josh
> On 4/30/21, 5:03 AM, " on behalf of José
> Villalaín" < on behalf of>
> wrote:
> Dear all,
> I am trying to build a system with two membranes in order to place
> different concentrations of ions (inside/outside). To do this, I have
> minimized, equilibrated and simulated a single membrane system
> (containing membrane, protein, ions and water).
> To obtain the system with two membranes, I use the previous system
> containing one membrane, duplicate it and join the two systems in one--00000000000007b51f05c131ed67--

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