System with two membranes

From: José Villalaín (
Date: Fri Apr 30 2021 - 03:54:08 CDT

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.
Afterwards, I remove all the water and ions, solvate with water, remove
the water inside the membrane and place the ions (different
concentrations inside and outside).

However, and although I have used several different parameters in the
configuration file (different constraints for water, lipids, ions and
their combinations, PME, not PME, pressure on /off), whenever I try to
equilibrate the system, it shrinks, specially the water molecules, and
the water and ions move to the sides and from the sides, move from/to
the different compartments .

So far it has been impossible for me to continue equilibrating the two
membrane system.

Could someone give me an idea of what I am doing wrong?.

Thank you very much in advance.

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